From 909faa7c1507008d0d6cd1ded5b7d528b60ee073 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:23:59 -0400 Subject: [PATCH 001/118] Create CODE_OF_CONDUCT.md --- CODE_OF_CONDUCT.md | 107 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 CODE_OF_CONDUCT.md diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 000000000..eedf973f8 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,107 @@ +## Code of Conduct + +Model Diagnostics Task Force framework team is dedicated to providing a respectful and inclusive community for everyone. We do not tolerate harassment or bullying of any community member in any form. This applies equally to all community members regardless of their title, seniority, background, gender, etc., in all forums managed by the MDTF framework team. This includes the mailing lists, our GitHub project space, slack workspaces, in-person events, and any other forums created by the project team. In addition, violations of this code outside these spaces may affect a person's ability to participate within them. As part of the code of conduct policy, we will provide below ground rules for all forums (e.g meetings) created by the project team, supporting project initiatives. + +## General code of conduct + +Our code of conduct policy for the project community members emphasizes on the following key ground rules: + +1. Respect everyone's opinion and privacy. +2. Every opinion has value. +3. Listen attentively to everyone's point of view. + +Furthermore, our community members are expected to adhere to the following: + +* **1. Be friendly, patient, and welcoming**. + We strive to be a community that welcomes and supports + people of all backgrounds and identities. This includes, but is not limited + to, members of any race, ethnicity, culture, national origin, color, + immigration status, social and economic class, educational level, sex, sexual + orientation, gender identity and expression, age, physical appearance, family + status, technological or professional choices, academic + discipline, religion, mental ability, and physical ability. + +* **2. Be considerate and respectful**. + Your work will be used by other people, and you in turn + will depend on the work of others. Any decision you take will affect users + and colleagues, and you should take those consequences into account when + making decisions. + Remember that we're a growing community with diverse members, and that you may be + communicating with someone with a different primary language or cultural + background. Not all of us will agree all the time, but disagreement is + no excuse for poor behavior or poor manners. + Do not insult or put down other community members. A community where people + feel uncomfortable or threatened is not a productive one. + + +* **3. Consider Impact vs. Intent**. + Disagreements, both social and + technical, happen all the time and Pangeo is no exception. + People perceive their own behaviors very differently than others perceive them. + What motivates one person may cause stress for another. + A few steps worth remembering include the following: + + * Other people do not see things the same way you do, + do not feel the same as you, or interpret the world the way you do. + Consider different people’s perspectives on things like change, + drive, structure, process, big picture, and small details. + * Ask for feedback and listen to them. + * Blaming each other doesn’t get us anywhere, while we can learn from mistakes to find better solutions. + +* **4. Moderate your expectations**. + Please respect that community members choose + how they spend their time in the project. A thoughtful question about your + expectations is preferable to demands for another person's time. + +* **5. A simple apology can go a long way**. + It can often de-escalate a situation, + and telling someone that you are sorry is an act of empathy that doesn’t + automatically imply an admission of guilt. + +* **6. Give due credit and avoid miscredit**. + +Motivate yourself and your community by acknowledging and giving credit to the original source, be it an individual-or-group, data-or-code, an inception of an idea, and so on, in different project forums. Discourage miscredit to foster a welcoming, inclusive environment. +We strive for the highest standards of scientific integrity. This includes sharing ideas and information, keeping accurate and complete records, and giving due credit to the contributions of others. Undisclosed conflicts of interest and scientific misconduct, including fabrication, falsification, and plagiarism, are incompatible with this code. + + +## Forms of harrassment + +We do not tolerate harassment or bullying of any community member in any form. +Forms of harrassment include, but is not limited to: + + * Violent threats or violent language directed against another person + * Discriminatory jokes and language + * Posting sexually explicit or violent material + * Posting (or threatening to post) other people's personally identifying + information ("doxing") + * Personal insults, especially those related to gender, + gender identity and expression, sexual orientation, ability, + physical appearance, body size, race, ethnicity, + religion, socioeconomic status, caste or creed + * Unwelcome sexual attention, stalking; + * Advocating for, or encouraging, any of the above behavior + * Repeated harassment of others. In general, if someone asks you to stop, + then stop + + +## How to Report Harassment and Discrimination + + + +## Review + +This code of conduct document will be reviewed periodically annually by the Model Diagnostics Task Force leads team members. + +## Your contributions + +Our community values every contribution to this open-source repository. Please follow the contributorship guidelines to see how you can contribute. +We encourage you to pitch in and join our growing community! + +### References + +This Code of Conduct has been adapted from: + * the [*Jupyter*](https://jupyter.org/governance/conduct/code_of_conduct.html) Project, licensed under a [*Creative Commons + Attribution*](http://creativecommons.org/licenses/by/3.0/) license. + * Pangeo (https://github.com/pangeo-data/.github/blob/main/CODE_OF_CONDUCT.md) + * The chemical professionals code of conduct (https://www.acs.org/content/acs/en/careers/career-services/ethics/the-chemical-professionals-code-of-conduct.html) +We are grateful to these projects for contributing these materials for us to easily reuse. From bcd70789b10f488b47cad9488e9c05f2930716e7 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:27:52 -0400 Subject: [PATCH 002/118] Update CODE_OF_CONDUCT.md --- CODE_OF_CONDUCT.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index eedf973f8..f02300cd7 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -86,7 +86,7 @@ Forms of harrassment include, but is not limited to: ## How to Report Harassment and Discrimination - +TBA ## Review @@ -94,7 +94,7 @@ This code of conduct document will be reviewed periodically annually by the Mode ## Your contributions -Our community values every contribution to this open-source repository. Please follow the contributorship guidelines to see how you can contribute. +Our community values every contribution to this open-source repository. Please follow the contributorship guidelines [in the works] to see how you can contribute. We encourage you to pitch in and join our growing community! ### References From 63e8a909c08c0390a65bb043a561530d3e185b1c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:30:08 -0400 Subject: [PATCH 003/118] Create .all-contributorsrc.json --- .all-contributorsrc.json | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 .all-contributorsrc.json diff --git a/.all-contributorsrc.json b/.all-contributorsrc.json new file mode 100644 index 000000000..81bbddb1c --- /dev/null +++ b/.all-contributorsrc.json @@ -0,0 +1,17 @@ +{ + "files": ["README.md"], + "imageSize": 100, + "contributorsPerLine": 7, + "contributorsSortAlphabetically": false, + "badgeTemplate": "[![All Contributors](https://img.shields.io/badge/all_contributors-<%= contributors.length %>-orange.svg?style=flat-square)](#contributors)", + "contributorTemplate": "\">\" width=\"<%= options.imageSize %>px;\" alt=\"\"/>
<%= contributor.name %>", + "types": { + "custom": { + "symbol": "🔭", + "description": "A custom contribution type.", + "link": "[<%= symbol %>](<%= url %> \"<%= description %>\")," + } + }, + "skipCi": "true", + "contributors": [] +} From f130392087415a5c8b8f9f4cd8b5cfe6b7215aaf Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:52:29 -0400 Subject: [PATCH 004/118] Create contributing.md --- contributing.md | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 contributing.md diff --git a/contributing.md b/contributing.md new file mode 100644 index 000000000..81fef8c43 --- /dev/null +++ b/contributing.md @@ -0,0 +1,49 @@ + +## How to contribute to MDTF framework + +#### **Did you find a bug?** + +* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/NOAA-GFDL/MDTF-diagnostics/issues?q=is%3Aissue+is%3Aopen). + +* If you're unable to find an open issue addressing the problem, [open a new one]([](https://github.com/NOAA-GFDL/MDTF-diagnostics/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring. + +* If relevant, use the bug report template that appears by default when you open a new issue. + +#### **Did you write a patch that fixes a bug?** + +* Open a new GitHub pull request with the patch. + +* Ensure the PR description clearly describes the problem and solution. Include the relevant issue number if applicable. + +* Before submitting, please read the [best practices](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_coding_tips.html?highlight=coding) guide to know more about coding conventions. Please note that this is a work in progress to set up best practices. +* Open a new issue to provide suggested changes to the best practices. + +#### **Did you fix whitespace, format code, or make a purely cosmetic patch?** + +Changes that are cosmetic in nature and do not add anything substantial to the stability, functionality, or testability of MDTF will still need an issue and go through a review process. + +#### **Do you intend to add a new feature or change an existing one?** + +* Suggest your change in the [GitHub discussions] (https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions) and start writing code. + +* Do not open an issue on GitHub until you have collected positive feedback about the change. GitHub issues are primarily intended for bug reports and fixes. + +#### **Do you have questions about the source code?** + +* Ask any question about how to use MDTF in the [GitHub discussions] (https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). +* Please do check out our [docs] (https://mdtf-diagnostics.readthedocs.io/en/latest/) to make sure it's not addressed already. But, please know that it's okay to ask us questions! We may redirect you to existing documentations and gather feedback to improve documentation. + +#### **Do you want to contribute to the MDTF documentation?** + +* Please start a [GitHub discussions] (https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). We would love your contribution in any form. + +#### ** Do you have a POD code submission that you'd like to contribute?** + +* Please double check the [POD development checklist] (https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_checklist.html?highlight=POD%20%20deve) +* Please check out this [cheatsheet] (https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_cheatsheet.html?highlight=cheatsheet) and start a PR! + +We encourage you to pitch in. Many thanks to our wonderful contributors [link tba] + +Thanks! + + From c24de91089322d76a8abec0eb88d84a7eb318920 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:53:42 -0400 Subject: [PATCH 005/118] Update contributing.md --- contributing.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/contributing.md b/contributing.md index 81fef8c43..257b43646 100644 --- a/contributing.md +++ b/contributing.md @@ -24,23 +24,23 @@ Changes that are cosmetic in nature and do not add anything substantial to the s #### **Do you intend to add a new feature or change an existing one?** -* Suggest your change in the [GitHub discussions] (https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions) and start writing code. +* Suggest your change in the [GitHub discussions](https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions) and start writing code. * Do not open an issue on GitHub until you have collected positive feedback about the change. GitHub issues are primarily intended for bug reports and fixes. #### **Do you have questions about the source code?** -* Ask any question about how to use MDTF in the [GitHub discussions] (https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). -* Please do check out our [docs] (https://mdtf-diagnostics.readthedocs.io/en/latest/) to make sure it's not addressed already. But, please know that it's okay to ask us questions! We may redirect you to existing documentations and gather feedback to improve documentation. +* Ask any question about how to use MDTF in the [GitHub discussions](https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). +* Please do check out our [docs](https://mdtf-diagnostics.readthedocs.io/en/latest/) to make sure it's not addressed already. But, please know that it's okay to ask us questions! We may redirect you to existing documentations and gather feedback to improve documentation. #### **Do you want to contribute to the MDTF documentation?** -* Please start a [GitHub discussions] (https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). We would love your contribution in any form. +* Please start a [GitHub discussions](https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). We would love your contribution in any form. #### ** Do you have a POD code submission that you'd like to contribute?** * Please double check the [POD development checklist] (https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_checklist.html?highlight=POD%20%20deve) -* Please check out this [cheatsheet] (https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_cheatsheet.html?highlight=cheatsheet) and start a PR! +* Please check out this [cheatsheet](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_cheatsheet.html?highlight=cheatsheet) and start a PR! We encourage you to pitch in. Many thanks to our wonderful contributors [link tba] From b68c9d28ea9edc3b9329266aebcd77d693b0e64d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:54:11 -0400 Subject: [PATCH 006/118] Update contributing.md --- contributing.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/contributing.md b/contributing.md index 257b43646..d20701d37 100644 --- a/contributing.md +++ b/contributing.md @@ -39,10 +39,10 @@ Changes that are cosmetic in nature and do not add anything substantial to the s #### ** Do you have a POD code submission that you'd like to contribute?** -* Please double check the [POD development checklist] (https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_checklist.html?highlight=POD%20%20deve) +* Please double check the [POD development checklist](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_checklist.html?highlight=POD%20%20deve) * Please check out this [cheatsheet](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_cheatsheet.html?highlight=cheatsheet) and start a PR! -We encourage you to pitch in. Many thanks to our wonderful contributors [link tba] +We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) Thanks! From 51b9c3fe8ab8f98faeb5cf74f81797c087848a62 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:55:53 -0400 Subject: [PATCH 007/118] Update contributing.md --- contributing.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/contributing.md b/contributing.md index d20701d37..48ad96311 100644 --- a/contributing.md +++ b/contributing.md @@ -1,4 +1,8 @@ + +[![All Contributors](https://img.shields.io/badge/all_contributors-2-orange.svg?style=flat-square)](#contributors-) + + ## How to contribute to MDTF framework #### **Did you find a bug?** From 66746bdd2d5340e8dac9f160c4c075b9377f9806 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:56:22 -0400 Subject: [PATCH 008/118] Update contributing.md --- contributing.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/contributing.md b/contributing.md index 48ad96311..d20701d37 100644 --- a/contributing.md +++ b/contributing.md @@ -1,8 +1,4 @@ - -[![All Contributors](https://img.shields.io/badge/all_contributors-2-orange.svg?style=flat-square)](#contributors-) - - ## How to contribute to MDTF framework #### **Did you find a bug?** From 40cf445c1ea6f6236ec01873c5a191ddd3d9a3cb Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 22:59:25 -0400 Subject: [PATCH 009/118] Update contributing.md --- contributing.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/contributing.md b/contributing.md index d20701d37..89289beca 100644 --- a/contributing.md +++ b/contributing.md @@ -42,6 +42,10 @@ Changes that are cosmetic in nature and do not add anything substantial to the s * Please double check the [POD development checklist](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_checklist.html?highlight=POD%20%20deve) * Please check out this [cheatsheet](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_cheatsheet.html?highlight=cheatsheet) and start a PR! +#### ** A word about code reviewers** + +Our code reviewers are presently part of the MDTF framework leads team. Their contributions are valuable! + We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) Thanks! From df231a88d710c9170deffb96117cdd6b7abafb75 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 19 Oct 2022 23:00:01 -0400 Subject: [PATCH 010/118] Update contributing.md @all-contributors please add @aradhakrishnanGFDL test test --- contributing.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contributing.md b/contributing.md index 89289beca..a2bf43dc5 100644 --- a/contributing.md +++ b/contributing.md @@ -9,7 +9,7 @@ * If relevant, use the bug report template that appears by default when you open a new issue. -#### **Did you write a patch that fixes a bug?** +#### **Did you write a patch that fixes a bug? ** * Open a new GitHub pull request with the patch. From 8b8b94f0550d8b54cfa09e2ce67d25c8afd500c7 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:32:29 -0400 Subject: [PATCH 011/118] Update README.md --- README.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/README.md b/README.md index 651ed4725..8166df4c9 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,21 @@ The MDTF-diagnostics package is a portable framework for running process-oriented diagnostics (PODs) on weather and climate model data. +## Contributors + + + + + + + + + + + +[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) + + ## What is a POD? ![MDTF_logo](<./doc/img/CPO_MAPP_MDTF_Logo.jpg>) Each process-oriented diagnostic [POD; [Maloney et al.(2019)](#citations)] targets a specific physical process or emergent behavior to determine how well one or more models represent the process, ensure that models produce the right answers for the right reasons, and identify gaps in the understanding of phenomena. Each POD is independent of other PODs. PODs generate diagnostic figures that can be viewed as an html file using a web browser. From 59d04184800a74f9223fcfcd4072d4c2f7127ef8 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:45:02 -0400 Subject: [PATCH 012/118] Update contributing.md --- contributing.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/contributing.md b/contributing.md index a2bf43dc5..0d441cfa5 100644 --- a/contributing.md +++ b/contributing.md @@ -48,6 +48,14 @@ Our code reviewers are presently part of the MDTF framework leads team. Their co We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) +#### ** How can I add myself to the contributors page?** + +Thank you for pitching in! Please check [this](https://allcontributors.org/docs/en/bot/usage) out to see how you can add your name to the contributor list. It's just one important step away! + +Create an issue or a PR and just add this "@all-contributors add @your_github_handle for doc" + +Please note that it can be a doc, design, idea, review, tool, talk, code or any contribution, any size! +Refer to [categories](https://allcontributors.org/docs/en/emoji-key) to see available categories. If you don't see a relevant one, open an issue please. Thanks! From d105370f4b504e269f076dcfc78998db0418b5a1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:45:38 -0400 Subject: [PATCH 013/118] Update contributing.md --- contributing.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/contributing.md b/contributing.md index 0d441cfa5..59b29cbca 100644 --- a/contributing.md +++ b/contributing.md @@ -9,7 +9,7 @@ * If relevant, use the bug report template that appears by default when you open a new issue. -#### **Did you write a patch that fixes a bug? ** +#### Did you write a patch that fixes a bug? * Open a new GitHub pull request with the patch. @@ -18,7 +18,7 @@ * Before submitting, please read the [best practices](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_coding_tips.html?highlight=coding) guide to know more about coding conventions. Please note that this is a work in progress to set up best practices. * Open a new issue to provide suggested changes to the best practices. -#### **Did you fix whitespace, format code, or make a purely cosmetic patch?** +#### Did you fix whitespace, format code, or make a purely cosmetic patch Changes that are cosmetic in nature and do not add anything substantial to the stability, functionality, or testability of MDTF will still need an issue and go through a review process. From 6050158babbb494077fdebb1a61a7a200a4937cf Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:46:38 -0400 Subject: [PATCH 014/118] Update contributing.md --- contributing.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/contributing.md b/contributing.md index 59b29cbca..dfb3e2791 100644 --- a/contributing.md +++ b/contributing.md @@ -22,33 +22,33 @@ Changes that are cosmetic in nature and do not add anything substantial to the stability, functionality, or testability of MDTF will still need an issue and go through a review process. -#### **Do you intend to add a new feature or change an existing one?** +#### Do you intend to add a new feature or change an existing one? * Suggest your change in the [GitHub discussions](https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions) and start writing code. * Do not open an issue on GitHub until you have collected positive feedback about the change. GitHub issues are primarily intended for bug reports and fixes. -#### **Do you have questions about the source code?** +#### Do you have questions about the source code? * Ask any question about how to use MDTF in the [GitHub discussions](https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). * Please do check out our [docs](https://mdtf-diagnostics.readthedocs.io/en/latest/) to make sure it's not addressed already. But, please know that it's okay to ask us questions! We may redirect you to existing documentations and gather feedback to improve documentation. -#### **Do you want to contribute to the MDTF documentation?** +#### Do you want to contribute to the MDTF documentation? * Please start a [GitHub discussions](https://github.com/NOAA-GFDL/MDTF-diagnostics/discussions). We would love your contribution in any form. -#### ** Do you have a POD code submission that you'd like to contribute?** +#### Do you have a POD code submission that you'd like to contribute? * Please double check the [POD development checklist](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_checklist.html?highlight=POD%20%20deve) * Please check out this [cheatsheet](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_cheatsheet.html?highlight=cheatsheet) and start a PR! -#### ** A word about code reviewers** +#### A word about code reviewers Our code reviewers are presently part of the MDTF framework leads team. Their contributions are valuable! We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) -#### ** How can I add myself to the contributors page?** +#### How can I add myself to the contributors page? Thank you for pitching in! Please check [this](https://allcontributors.org/docs/en/bot/usage) out to see how you can add your name to the contributor list. It's just one important step away! From fea552e26323c36f4aab143044e3bce59ca0ef1c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:50:26 -0400 Subject: [PATCH 015/118] Update contributing.md @all-contributors add @aradhakrishnanGFDL for doc --- contributing.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contributing.md b/contributing.md index dfb3e2791..e5f360fd8 100644 --- a/contributing.md +++ b/contributing.md @@ -1,7 +1,7 @@ ## How to contribute to MDTF framework -#### **Did you find a bug?** +#### Did you find a bug? * **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/NOAA-GFDL/MDTF-diagnostics/issues?q=is%3Aissue+is%3Aopen). From 9a65b7d582dafe1299a6c9d73493252dd8e07205 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:52:38 -0400 Subject: [PATCH 016/118] Update README.md --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 8166df4c9..c29694259 100644 --- a/README.md +++ b/README.md @@ -9,16 +9,18 @@ The MDTF-diagnostics package is a portable framework for running process-oriente + + + + + +

Aparna Radhakrishnan
👀
Jess
💻
- -[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) - - ## What is a POD? ![MDTF_logo](<./doc/img/CPO_MAPP_MDTF_Logo.jpg>) Each process-oriented diagnostic [POD; [Maloney et al.(2019)](#citations)] targets a specific physical process or emergent behavior to determine how well one or more models represent the process, ensure that models produce the right answers for the right reasons, and identify gaps in the understanding of phenomena. Each POD is independent of other PODs. PODs generate diagnostic figures that can be viewed as an html file using a web browser. From eef9eb9b9eeafed512db859871447265c6bb7192 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:54:51 -0400 Subject: [PATCH 017/118] Update README.md --- README.md | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/README.md b/README.md index c29694259..651ed4725 100644 --- a/README.md +++ b/README.md @@ -4,23 +4,6 @@ The MDTF-diagnostics package is a portable framework for running process-oriented diagnostics (PODs) on weather and climate model data. -## Contributors - - - - - - - - - -

Aparna Radhakrishnan
👀
Jess
💻
- - - - - - ## What is a POD? ![MDTF_logo](<./doc/img/CPO_MAPP_MDTF_Logo.jpg>) Each process-oriented diagnostic [POD; [Maloney et al.(2019)](#citations)] targets a specific physical process or emergent behavior to determine how well one or more models represent the process, ensure that models produce the right answers for the right reasons, and identify gaps in the understanding of phenomena. Each POD is independent of other PODs. PODs generate diagnostic figures that can be viewed as an html file using a web browser. From a3acbafa3bb57b2f885633fb58fadbe4a408af44 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 11:56:09 -0400 Subject: [PATCH 018/118] Update contributing.md --- contributing.md | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/contributing.md b/contributing.md index e5f360fd8..df76b9efe 100644 --- a/contributing.md +++ b/contributing.md @@ -46,8 +46,6 @@ Changes that are cosmetic in nature and do not add anything substantial to the s Our code reviewers are presently part of the MDTF framework leads team. Their contributions are valuable! -We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) - #### How can I add myself to the contributors page? Thank you for pitching in! Please check [this](https://allcontributors.org/docs/en/bot/usage) out to see how you can add your name to the contributor list. It's just one important step away! @@ -58,4 +56,17 @@ Please note that it can be a doc, design, idea, review, tool, talk, code or any Refer to [categories](https://allcontributors.org/docs/en/emoji-key) to see available categories. If you don't see a relevant one, open an issue please. Thanks! +#### THANK YOU + +We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) + +## Contributors + + + + + + + + From 6d01c1e3311747216295bd270576672e55e40811 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 12:41:15 -0400 Subject: [PATCH 019/118] Update README.md --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 651ed4725..804dd674c 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,10 @@ The MDTF-diagnostics package is a portable framework for running process-oriented diagnostics (PODs) on weather and climate model data. + +[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) + + ## What is a POD? ![MDTF_logo](<./doc/img/CPO_MAPP_MDTF_Logo.jpg>) Each process-oriented diagnostic [POD; [Maloney et al.(2019)](#citations)] targets a specific physical process or emergent behavior to determine how well one or more models represent the process, ensure that models produce the right answers for the right reasons, and identify gaps in the understanding of phenomena. Each POD is independent of other PODs. PODs generate diagnostic figures that can be viewed as an html file using a web browser. From 225fa41b9185ded1f2c80b58e2b7fb25680bf083 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Thu, 20 Oct 2022 16:58:14 +0000 Subject: [PATCH 020/118] docs: update README.md [skip ci] --- README.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/README.md b/README.md index 651ed4725..55c14450b 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,7 @@ # MDTF-diagnostics: A Portable Framework for Weather and Climate Model Data Analysis + +[![All Contributors](https://img.shields.io/badge/all_contributors-1-orange.svg?style=flat-square)](#contributors-) + [![Documentation Status](https://readthedocs.org/projects/mdtf-diagnostics/badge/?version=latest)](https://mdtf-diagnostics.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics.svg?branch=main)](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics) [![Total alerts](https://img.shields.io/lgtm/alerts/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/alerts/) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/context:python) @@ -201,3 +204,25 @@ E. D. Maloney et al. (2019): Process-Oriented Evaluation of Climate and Weather ## Disclaimer This repository is a scientific product and is not an official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government. + +## Contributors ✨ + +Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)): + + + + + + + + + + +
John Krasting
John Krasting
⚠️ 🤔
+ + + + + + +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! \ No newline at end of file From a2fe3b2068316e8f78a1adbf341708bd689a885e Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Thu, 20 Oct 2022 16:58:15 +0000 Subject: [PATCH 021/118] docs: create .all-contributorsrc [skip ci] --- .all-contributorsrc | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 .all-contributorsrc diff --git a/.all-contributorsrc b/.all-contributorsrc new file mode 100644 index 000000000..089106101 --- /dev/null +++ b/.all-contributorsrc @@ -0,0 +1,26 @@ +{ + "files": [ + "README.md" + ], + "imageSize": 100, + "commit": false, + "commitConvention": "angular", + "contributors": [ + { + "login": "jkrasting", + "name": "John Krasting", + "avatar_url": "https://avatars.githubusercontent.com/u/6594675?v=4", + "profile": "http://www.gfdl.noaa.gov/john-krasting-homepage", + "contributions": [ + "test", + "ideas" + ] + } + ], + "contributorsPerLine": 7, + "skipCi": true, + "repoType": "github", + "repoHost": "https://github.com", + "projectName": "MDTF-diagnostics", + "projectOwner": "aradhakrishnanGFDL" +} From 8fa3cb1deca0c500be02719ee51f511bd9cdeb64 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 13:32:49 -0400 Subject: [PATCH 022/118] Update contributing.md --- contributing.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/contributing.md b/contributing.md index df76b9efe..bf584e68e 100644 --- a/contributing.md +++ b/contributing.md @@ -60,6 +60,10 @@ Thanks! We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) + +[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) + + ## Contributors From 50288009371b65624fb3e1f0a736a9fbea315824 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 13:34:53 -0400 Subject: [PATCH 023/118] Update README.md --- README.md | 24 +----------------------- 1 file changed, 1 insertion(+), 23 deletions(-) diff --git a/README.md b/README.md index c8a14e4ee..f40e69b89 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,4 @@ # MDTF-diagnostics: A Portable Framework for Weather and Climate Model Data Analysis - -[![All Contributors](https://img.shields.io/badge/all_contributors-1-orange.svg?style=flat-square)](#contributors-) - [![Documentation Status](https://readthedocs.org/projects/mdtf-diagnostics/badge/?version=latest)](https://mdtf-diagnostics.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics.svg?branch=main)](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics) [![Total alerts](https://img.shields.io/lgtm/alerts/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/alerts/) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/context:python) @@ -209,24 +206,5 @@ E. D. Maloney et al. (2019): Process-Oriented Evaluation of Climate and Weather This repository is a scientific product and is not an official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government. -## Contributors ✨ - -Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)): - - - - - - - - - - -
John Krasting
John Krasting
⚠️ 🤔
- - - - - -This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! \ No newline at end of file +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! From 94264f9d633ea10cb74d96ee5184879c05847c7b Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 13:35:11 -0400 Subject: [PATCH 024/118] Update README.md --- README.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/README.md b/README.md index f40e69b89..89a23de73 100644 --- a/README.md +++ b/README.md @@ -4,10 +4,6 @@ The MDTF-diagnostics package is a portable framework for running process-oriented diagnostics (PODs) on weather and climate model data. - -[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) - - ## What is a POD? ![MDTF_logo](<./doc/img/CPO_MAPP_MDTF_Logo.jpg>) Each process-oriented diagnostic [POD; [Maloney et al.(2019)](#citations)] targets a specific physical process or emergent behavior to determine how well one or more models represent the process, ensure that models produce the right answers for the right reasons, and identify gaps in the understanding of phenomena. Each POD is independent of other PODs. PODs generate diagnostic figures that can be viewed as an html file using a web browser. From 1cd645c848217bae84751bdbc7bae254a67d6c37 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 13:36:31 -0400 Subject: [PATCH 025/118] Update contributing.md --- contributing.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/contributing.md b/contributing.md index bf584e68e..51893e1bf 100644 --- a/contributing.md +++ b/contributing.md @@ -58,11 +58,8 @@ Thanks! #### THANK YOU -We encourage you to pitch in. Many thanks to our wonderful [contributors](link tba) +We encourage you to pitch in. Many thanks to our wonderful [contributors] - -[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) - ## Contributors @@ -74,3 +71,8 @@ We encourage you to pitch in. Many thanks to our wonderful [contributors](link t + + + +[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) + From 76ab4d45da2869c8111dc74314b4d9dff364a0ec Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 13:37:15 -0400 Subject: [PATCH 026/118] Update .all-contributorsrc.json --- .all-contributorsrc.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.all-contributorsrc.json b/.all-contributorsrc.json index 81bbddb1c..5bd67f7b6 100644 --- a/.all-contributorsrc.json +++ b/.all-contributorsrc.json @@ -1,5 +1,5 @@ { - "files": ["README.md"], + "files": ["contributing.md"], "imageSize": 100, "contributorsPerLine": 7, "contributorsSortAlphabetically": false, From c69ac1ca4657d0a8c45ae583b1e01f5e882afc3b Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 13:37:42 -0400 Subject: [PATCH 027/118] Update .all-contributorsrc --- .all-contributorsrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 089106101..a4f38e0c4 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -1,6 +1,6 @@ { "files": [ - "README.md" + "contributing.md" ], "imageSize": 100, "commit": false, From 5a81fdbe4821c30f05b333feded1fbb33673149f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 13:38:19 -0400 Subject: [PATCH 028/118] Update .all-contributorsrc start fresh --- .all-contributorsrc | 27 +-------------------------- 1 file changed, 1 insertion(+), 26 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index a4f38e0c4..8b1378917 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -1,26 +1 @@ -{ - "files": [ - "contributing.md" - ], - "imageSize": 100, - "commit": false, - "commitConvention": "angular", - "contributors": [ - { - "login": "jkrasting", - "name": "John Krasting", - "avatar_url": "https://avatars.githubusercontent.com/u/6594675?v=4", - "profile": "http://www.gfdl.noaa.gov/john-krasting-homepage", - "contributions": [ - "test", - "ideas" - ] - } - ], - "contributorsPerLine": 7, - "skipCi": true, - "repoType": "github", - "repoHost": "https://github.com", - "projectName": "MDTF-diagnostics", - "projectOwner": "aradhakrishnanGFDL" -} + From 9570a1325cc16ff97c96408d4163f9a1cb1cacf2 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 14:19:45 -0400 Subject: [PATCH 029/118] Delete .all-contributorsrc --- .all-contributorsrc | 1 - 1 file changed, 1 deletion(-) delete mode 100644 .all-contributorsrc diff --git a/.all-contributorsrc b/.all-contributorsrc deleted file mode 100644 index 8b1378917..000000000 --- a/.all-contributorsrc +++ /dev/null @@ -1 +0,0 @@ - From 3de797a483e16c7dcf0c3db5d9f1386222ab61a6 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 14:22:09 -0400 Subject: [PATCH 030/118] Update .all-contributorsrc.json --- .all-contributorsrc.json | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/.all-contributorsrc.json b/.all-contributorsrc.json index 5bd67f7b6..2e19299d6 100644 --- a/.all-contributorsrc.json +++ b/.all-contributorsrc.json @@ -1,6 +1,11 @@ { - "files": ["contributing.md"], + "projectName": "all-contributors", + "projectOwner": "all-contributors", + "repoType": "github", + "repoHost": "https://github.com", + "files": ["README.md"], "imageSize": 100, + "commit": false, "contributorsPerLine": 7, "contributorsSortAlphabetically": false, "badgeTemplate": "[![All Contributors](https://img.shields.io/badge/all_contributors-<%= contributors.length %>-orange.svg?style=flat-square)](#contributors)", @@ -12,6 +17,7 @@ "link": "[<%= symbol %>](<%= url %> \"<%= description %>\")," } }, - "skipCi": "true", + "linkToUsage": true, + "skipCi": true, "contributors": [] } From 9bfdacb4737ff985cb25ff8314e292fee9470516 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 14:24:18 -0400 Subject: [PATCH 031/118] Update README.md --- README.md | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 89a23de73..8a8c71b20 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ # MDTF-diagnostics: A Portable Framework for Weather and Climate Model Data Analysis -[![Documentation Status](https://readthedocs.org/projects/mdtf-diagnostics/badge/?version=latest)](https://mdtf-diagnostics.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics.svg?branch=main)](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics) [![Total alerts](https://img.shields.io/lgtm/alerts/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/alerts/) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/context:python) +[![Documentation Status](https://readthedocs.org/projects/mdtf-diagnostics/badge/?version=latest)](https://mdtf-diagnostics.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics.svg?branch=main)](https://travis-ci.com/NOAA-GFDL/MDTF-diagnostics) [![Total alerts](https://img.shields.io/lgtm/alerts/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/alerts/) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/NOAA-GFDL/MDTF-diagnostics.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/NOAA-GFDL/MDTF-diagnostics/context:python)[![All Contributors](https://img.shields.io/badge/all_contributors-13-orange.svg?style=flat-square)](#contributors) + + The MDTF-diagnostics package is a portable framework for running process-oriented diagnostics (PODs) on weather and climate model data. @@ -204,3 +206,14 @@ This repository is a scientific product and is not an official communication of This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! + +## Contributors + + + + + + + + + From fd4b6e7365e8537c0289212b67113a0f7e268b40 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 14:27:11 -0400 Subject: [PATCH 032/118] Create CONTRIBUTORS.md --- CONTRIBUTORS.md | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 CONTRIBUTORS.md diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md new file mode 100644 index 000000000..b6a2be898 --- /dev/null +++ b/CONTRIBUTORS.md @@ -0,0 +1,10 @@ +## Contributors + + + + + + + + + From 4e7d9c8daadd3e5003719c8ad2ecfcce38784795 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 14:27:28 -0400 Subject: [PATCH 033/118] Update .all-contributorsrc.json --- .all-contributorsrc.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.all-contributorsrc.json b/.all-contributorsrc.json index 2e19299d6..fe0787249 100644 --- a/.all-contributorsrc.json +++ b/.all-contributorsrc.json @@ -3,7 +3,7 @@ "projectOwner": "all-contributors", "repoType": "github", "repoHost": "https://github.com", - "files": ["README.md"], + "files": ["CONTRIBUTORS.md"], "imageSize": 100, "commit": false, "contributorsPerLine": 7, From c746016812cb08a8973bb0c97876d50102cbfa5e Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 20 Oct 2022 14:27:45 -0400 Subject: [PATCH 034/118] Update README.md --- README.md | 9 --------- 1 file changed, 9 deletions(-) diff --git a/README.md b/README.md index 8a8c71b20..df8f13077 100644 --- a/README.md +++ b/README.md @@ -207,13 +207,4 @@ This repository is a scientific product and is not an official communication of This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! -## Contributors - - - - - - - - From 202e4ebec2b213aab64522d398b990da23953cc7 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 26 Oct 2022 17:09:46 -0400 Subject: [PATCH 035/118] Create main.yml --- .github/workflows/main.yml | 69 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 .github/workflows/main.yml diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 000000000..cbc155734 --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,69 @@ +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Deploy to ECS,open + +on: + push: + branches: + - main + +env: + AWS_REGION: us-east-1 # set this to your preferred AWS region, e.g. us-west-1 + ECR_REPOSITORY: mdtf/mdtf-test # set this to your Amazon ECR repository name + ECS_SERVICE: custom-service # MY_ECS_SERVICE set this to your Amazon ECS service name + ECS_CLUSTER: mdtf-east1 # MY_ECS_CLUSTER set this to your Amazon ECS cluster name + ECS_TASK_DEFINITION: ecs-task-defn.json # set this to the path to your Amazon ECS task definition + # file, e.g. .aws/task-definition.json + CONTAINER_NAME: mdtf-test-a1r # set this to the name of the container in the + # containerDefinitions section of your task definition MY_CONTAINER_NAME + +jobs: + deploy: + name: push-to-public-ecr-cache-test + runs-on: ubuntu-latest + environment: dev + + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@13d241b293754004c80624b5567555c4a39ffbe3 + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: ${{ env.AWS_REGION }} + + - name: Build, tag, and push image to Amazon ECR + id: build-image + uses: aradhakrishnanGFDL/docker-build-with-cache-action@master #support-aws-ecr-public + env: + ECR_REGISTRY: public.ecr.aws + IMAGE_TAG: "latest" + ECS_IMAGE: $ECR_REGISTRY/ECR_REPOSITORY:$env.IMAGE_TAG + with: + registry: public.ecr.aws + username: "${{ secrets.AWS_ACCESS_KEY_ID }}" + password: "${{ secrets.AWS_SECRET_ACCESS_KEY }}" + image_name: c6h4h4s8/mdtf/mdtf-test + push_image_and_stages: true + image_tag: latest + + - name: Fill in the new image ID in the Amazon ECS task definition + id: task-def + uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a + with: + task-definition: ${{ env.ECS_TASK_DEFINITION }} + container-name: ${{ env.CONTAINER_NAME }} + image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest + + - name: Deploy Amazon ECS task definition + uses: aws-actions/amazon-ecs-deploy-task-definition@de0132cf8cdedb79975c6d42b77eb7ea193cf28e + with: + task-definition: ${{ steps.task-def.outputs.task-definition }} + service: ${{ env.ECS_SERVICE }} + cluster: ${{ env.ECS_CLUSTER }} + wait-for-service-stability: true From 840ba2508ada1e8850169fe56b0338b71ac9e6f1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 26 Oct 2022 17:15:28 -0400 Subject: [PATCH 036/118] Create Dockerfile --- Dockerfile | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 000000000..0170421ca --- /dev/null +++ b/Dockerfile @@ -0,0 +1,47 @@ +# Base OS +FROM ubuntu:20.04 +# Container Metadata +LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" +LABEL version="alpha-01" +LABEL description="This is a docker image for the MDTF-diagnostics package" +# Disable Prompt During Packages Installation +ARG DEBIAN_FRONTEND=noninteractive +# Update Ubuntu Software repository +RUN apt update +# Install dependencies +RUN apt install -y wget +RUN apt install -y vim +# Cleanup +RUN rm -rf /var/lib/apt/lists/* && \ + apt clean +# Install Miniconda3 +# Download the latest shell script +RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +# Change permission to execute build script +RUN chmod +x Miniconda3-latest-Linux-x86_64.sh +# Run miniconda installation script +ENV PATH="/root/miniconda3/bin:${PATH}" +ARG PATH="/root/miniconda3/bin:${PATH}" +RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b +RUN rm -f Miniconda3-latest-Linux-x86_64.sh +RUN conda info +RUN conda init bash +RUN conda install -c conda-forge mamba +# Copy the MDTF-diagnostics package contents from local machine to image +ENV CODE_ROOT=/proj/MDTF-diagnostics +COPY src ${CODE_ROOT}/src +COPY data ${CODE_ROOT}/data +#COPY diagnostics ${CODE_ROOT}/diagnostics +COPY mdtf_framework.py ${CODE_ROOT} +COPY shared ${CODE_ROOT}/shared +COPY sites ${CODE_ROOT}/sites +COPY tests ${CODE_ROOT}/tests +# Install conda environments +ENV CONDA_ROOT=/root/miniconda3 +ENV CONDA_ENV_DIR=/root/miniconda3/envs +RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ + --conda_env_dir ${CONDA_ENV_DIR} +# Verify installation +RUN ${CODE_ROOT}/mdtf --version +# Run mdtf on src/default_tests.jsonc +CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] From dbb35b7dba0433ea69837e34d00b7588efcc8121 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 27 Oct 2022 15:51:28 -0400 Subject: [PATCH 037/118] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 0170421ca..4c7ff9ad6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,6 +11,7 @@ RUN apt update # Install dependencies RUN apt install -y wget RUN apt install -y vim +RUN apt install -y git # Cleanup RUN rm -rf /var/lib/apt/lists/* && \ apt clean From b11ee391dc0b6d5d817e88aff113cb044fac5363 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 11:29:13 -0400 Subject: [PATCH 038/118] Update main.yml --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index cbc155734..9ee9f6054 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -3,7 +3,7 @@ # separate terms of service, privacy policy, and support # documentation. -name: Deploy to ECS,open +name: Deploy to ECS. Build, push image, on: push: From c134a4dc38af7517b010e03a3d257fca43ddbe52 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 11:31:01 -0400 Subject: [PATCH 039/118] Update main.yml on PR --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9ee9f6054..08afe9f16 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -6,7 +6,7 @@ name: Deploy to ECS. Build, push image, on: - push: + pull_request: branches: - main From e814fc40fff99ed338fc2cf7b024bccb2c3093ee Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 11:49:23 -0400 Subject: [PATCH 040/118] Update Dockerfile env_dir --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4c7ff9ad6..b8b898811 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,7 +41,7 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ - --conda_env_dir ${CONDA_ENV_DIR} + --env_dir ${CONDA_ENV_DIR} # Verify installation RUN ${CODE_ROOT}/mdtf --version # Run mdtf on src/default_tests.jsonc From d64bcb7559ef16d2f24018d285a328457720839a Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 14:40:25 -0400 Subject: [PATCH 041/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b8b898811..0d91945c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # Base OS -FROM ubuntu:20.04 +FROM ubuntu:latest # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" From e52f0ce25dafe9d97cc5256c02cba12190f236d1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 14:59:29 -0400 Subject: [PATCH 042/118] Update Dockerfile libarchive --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 0d91945c4..b2e445214 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,6 +40,7 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs +conda install libarchive -n base -c conda-forge #workaround RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From 608e9164269bb3759cba465e5bb674ac86635e4d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 15:04:48 -0400 Subject: [PATCH 043/118] Update Dockerfile --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b2e445214..3bb804fbd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,7 +40,8 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs -conda install libarchive -n base -c conda-forge #workaround +#workaround +conda install libarchive -n base -c conda-forge RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From 0e579e0eb2d1d89c9bbbed85d3b69af7dc922671 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 15:09:49 -0400 Subject: [PATCH 044/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3bb804fbd..bb1450961 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,7 +41,7 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs #workaround -conda install libarchive -n base -c conda-forge +mamba install libarchive -n base -c conda-forge RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From fc408a8e1fa37f52fc413cd89581de047013d146 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 15:28:00 -0400 Subject: [PATCH 045/118] Update Dockerfile --- Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index bb1450961..0d91945c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,8 +40,6 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs -#workaround -mamba install libarchive -n base -c conda-forge RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From 203b19f2326cd274ecece254089cb65d2d67659e Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 11:57:09 -0400 Subject: [PATCH 046/118] Update Dockerfile mamba version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0d91945c4..585eaad80 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,7 +27,7 @@ RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN conda info RUN conda init bash -RUN conda install -c conda-forge mamba +RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src From dedfe71611a80634a6196865127b6d77e66e957a Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 16:36:38 -0400 Subject: [PATCH 047/118] Update Dockerfile --- Dockerfile | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index 585eaad80..1413b4bea 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,6 @@ # Base OS FROM ubuntu:latest +FROM continuumio/miniconda3 # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" @@ -17,14 +18,14 @@ RUN rm -rf /var/lib/apt/lists/* && \ apt clean # Install Miniconda3 # Download the latest shell script -RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -# Change permission to execute build script -RUN chmod +x Miniconda3-latest-Linux-x86_64.sh -# Run miniconda installation script -ENV PATH="/root/miniconda3/bin:${PATH}" -ARG PATH="/root/miniconda3/bin:${PATH}" -RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b -RUN rm -f Miniconda3-latest-Linux-x86_64.sh +####RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +#### Change permission to execute build script +####RUN chmod +x Miniconda3-latest-Linux-x86_64.sh +#### Run miniconda installation script +####ENV PATH="/root/miniconda3/bin:${PATH}" +####ARG PATH="/root/miniconda3/bin:${PATH}" +####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b +####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN conda info RUN conda init bash RUN conda install 'mamba<=1.4.5' -n base -c conda-forge @@ -40,6 +41,7 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs +RUN conda install -c conda-forge -c default libarchive RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From cfc4362879f19c78183ed6b91cac887f85244b1c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 16:50:05 -0400 Subject: [PATCH 048/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 1413b4bea..b3a21c082 100644 --- a/Dockerfile +++ b/Dockerfile @@ -28,7 +28,7 @@ RUN rm -rf /var/lib/apt/lists/* && \ ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN conda info RUN conda init bash -RUN conda install 'mamba<=1.4.5' -n base -c conda-forge +##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src From 7478cdf08e75c1ebcb7c1b5c46b3dcd45c0869aa Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 16:57:59 -0400 Subject: [PATCH 049/118] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index b3a21c082..47776cbaf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -39,8 +39,8 @@ COPY shared ${CODE_ROOT}/shared COPY sites ${CODE_ROOT}/sites COPY tests ${CODE_ROOT}/tests # Install conda environments -ENV CONDA_ROOT=/root/miniconda3 -ENV CONDA_ENV_DIR=/root/miniconda3/envs +ENV CONDA_ROOT=/opt/conda/ +ENV CONDA_ENV_DIR=/opt/conda/envs RUN conda install -c conda-forge -c default libarchive RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} From 951296d2858102e8b00c9b7bdfd5366ce00dddc7 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 17:42:22 -0400 Subject: [PATCH 050/118] Create ecs-task-defn.json --- ecs-task-defn.json | 118 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 ecs-task-defn.json diff --git a/ecs-task-defn.json b/ecs-task-defn.json new file mode 100644 index 000000000..fe676c693 --- /dev/null +++ b/ecs-task-defn.json @@ -0,0 +1,118 @@ +{ + "ipcMode": null, + "executionRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", + "containerDefinitions": [ + { + "dnsSearchDomains": null, + "environmentFiles": null, + "logConfiguration": { + "logDriver": "awslogs", + "secretOptions": null, + "options": { + "awslogs-group": "/ecs/first-run-task-definition", + "awslogs-region": "us-east-2", + "awslogs-stream-prefix": "ecs" + } + }, + "entryPoint": [], + "portMappings": [], + "command": [], + "linuxParameters": null, + "cpu": 0, + "environment": [], + "resourceRequirements": null, + "ulimits": null, + "dnsServers": null, + "mountPoints": [], + "workingDirectory": null, + "secrets": null, + "dockerSecurityOptions": null, + "memory": null, + "memoryReservation": null, + "volumesFrom": [], + "stopTimeout": null, + "image": "430073024411.dkr.ecr.us-east-1.amazonaws.com/wrongkindofdoctor/mdtf-test:latest", + "startTimeout": null, + "firelensConfiguration": null, + "dependsOn": null, + "disableNetworking": null, + "interactive": null, + "healthCheck": null, + "essential": true, + "links": [], + "hostname": null, + "extraHosts": null, + "pseudoTerminal": null, + "user": null, + "readonlyRootFilesystem": null, + "dockerLabels": null, + "systemControls": null, + "privileged": null, + "name": "custom" + } + ], + "placementConstraints": [], + "memory": "512", + "taskRoleArn": null, + "compatibilities": [ + "EC2", + "FARGATE" + ], + "taskDefinitionArn": "arn:aws:ecs:us-east-2:430073024411:task-definition/first-run-task-definition:1", + "family": "first-run-task-definition", + "requiresAttributes": [ + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.logging-driver.awslogs" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "ecs.capability.execution-role-awslogs" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.ecr-auth" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.19" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "ecs.capability.execution-role-ecr-pull" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.18" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "ecs.capability.task-eni" + } + ], + "pidMode": null, + "requiresCompatibilities": [ + "FARGATE" + ], + "networkMode": "awsvpc", + "cpu": "256", + "revision": 1, + "status": "ACTIVE", + "inferenceAccelerators": null, + "proxyConfiguration": null, + "volumes": [] +} From 0b67ac4835d7e0ea2adf5c5a820d9b832fba3385 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:20:15 -0400 Subject: [PATCH 051/118] Update ecs-task-defn.json mdtf-test task --- ecs-task-defn.json | 175 ++++++++++++++++----------------------------- 1 file changed, 60 insertions(+), 115 deletions(-) diff --git a/ecs-task-defn.json b/ecs-task-defn.json index fe676c693..b8fefe348 100644 --- a/ecs-task-defn.json +++ b/ecs-task-defn.json @@ -1,118 +1,63 @@ { - "ipcMode": null, - "executionRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", - "containerDefinitions": [ - { - "dnsSearchDomains": null, - "environmentFiles": null, - "logConfiguration": { - "logDriver": "awslogs", - "secretOptions": null, - "options": { - "awslogs-group": "/ecs/first-run-task-definition", - "awslogs-region": "us-east-2", - "awslogs-stream-prefix": "ecs" + "taskDefinitionArn": "arn:aws:ecs:us-east-1:430073024411:task-definition/mdtf-test-a1r:25", + "containerDefinitions": [ + { + "name": "mdtf-test-a1r", + "image": "public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest", + "cpu": 0, + "portMappings": [], + "essential": true, + "environment": [], + "mountPoints": [], + "volumesFrom": [], + "logConfiguration": { + "logDriver": "awslogs", + "options": { + "awslogs-group": "/ecs/mdtf-test-a1r", + "awslogs-region": "us-east-1", + "awslogs-stream-prefix": "ecs" + } + } } - }, - "entryPoint": [], - "portMappings": [], - "command": [], - "linuxParameters": null, - "cpu": 0, - "environment": [], - "resourceRequirements": null, - "ulimits": null, - "dnsServers": null, - "mountPoints": [], - "workingDirectory": null, - "secrets": null, - "dockerSecurityOptions": null, - "memory": null, - "memoryReservation": null, - "volumesFrom": [], - "stopTimeout": null, - "image": "430073024411.dkr.ecr.us-east-1.amazonaws.com/wrongkindofdoctor/mdtf-test:latest", - "startTimeout": null, - "firelensConfiguration": null, - "dependsOn": null, - "disableNetworking": null, - "interactive": null, - "healthCheck": null, - "essential": true, - "links": [], - "hostname": null, - "extraHosts": null, - "pseudoTerminal": null, - "user": null, - "readonlyRootFilesystem": null, - "dockerLabels": null, - "systemControls": null, - "privileged": null, - "name": "custom" - } - ], - "placementConstraints": [], - "memory": "512", - "taskRoleArn": null, - "compatibilities": [ - "EC2", - "FARGATE" - ], - "taskDefinitionArn": "arn:aws:ecs:us-east-2:430073024411:task-definition/first-run-task-definition:1", - "family": "first-run-task-definition", - "requiresAttributes": [ - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.logging-driver.awslogs" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "ecs.capability.execution-role-awslogs" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.ecr-auth" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.docker-remote-api.1.19" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "ecs.capability.execution-role-ecr-pull" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.docker-remote-api.1.18" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "ecs.capability.task-eni" - } - ], - "pidMode": null, - "requiresCompatibilities": [ - "FARGATE" - ], - "networkMode": "awsvpc", - "cpu": "256", - "revision": 1, - "status": "ACTIVE", - "inferenceAccelerators": null, - "proxyConfiguration": null, - "volumes": [] + ], + "family": "mdtf-test-a1r", + "taskRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", + "executionRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", + "networkMode": "awsvpc", + "revision": 25, + "volumes": [], + "status": "ACTIVE", + "requiresAttributes": [ + { + "name": "com.amazonaws.ecs.capability.logging-driver.awslogs" + }, + { + "name": "ecs.capability.execution-role-awslogs" + }, + { + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.19" + }, + { + "name": "com.amazonaws.ecs.capability.task-iam-role" + }, + { + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.18" + }, + { + "name": "ecs.capability.task-eni" + } + ], + "placementConstraints": [], + "compatibilities": [ + "EC2", + "FARGATE" + ], + "requiresCompatibilities": [ + "FARGATE" + ], + "cpu": "4096", + "memory": "8192", + "registeredAt": "2022-10-20T16:01:08.915Z", + "registeredBy": "arn:aws:iam::430073024411:user/a1r", + "tags": [] } From bd23c11d07b00c99f0eab21a0d5c1073a56a06f4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:21:42 -0400 Subject: [PATCH 052/118] Update Dockerfile --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 47776cbaf..354bdf507 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,8 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs RUN conda install -c conda-forge -c default libarchive -RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ +#add base only for testing +RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation RUN ${CODE_ROOT}/mdtf --version From d901b70b1bcd587484a9aa3dcb701ee426a8ced9 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:26:04 -0400 Subject: [PATCH 053/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 354bdf507..d8be707ed 100644 --- a/Dockerfile +++ b/Dockerfile @@ -46,6 +46,6 @@ RUN conda install -c conda-forge -c default libarchive RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation -RUN ${CODE_ROOT}/mdtf --version +RUN /proj/MDTF-diagnostics/mdtf --version # Run mdtf on src/default_tests.jsonc CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] From 9c09ed764325c1730240837475346ef504e7eccc Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:46:06 -0400 Subject: [PATCH 054/118] Update Dockerfile --- Dockerfile | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index d8be707ed..3b29e3b4b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM continuumio/miniconda3 +FROM mamba-org/micromamba-docker:latest # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" @@ -41,10 +41,12 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -RUN conda install -c conda-forge -c default libarchive +#what-really RUN conda install -c conda-forge -c default libarchive +micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + #add base only for testing -RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ - --env_dir ${CONDA_ENV_DIR} +#c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ +#c --env_dir ${CONDA_ENV_DIR} # Verify installation RUN /proj/MDTF-diagnostics/mdtf --version # Run mdtf on src/default_tests.jsonc From 1b99e7ab3e3282955553bcf0465c5a078eb311cd Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:49:47 -0400 Subject: [PATCH 055/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3b29e3b4b..52de77b33 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,7 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs #what-really RUN conda install -c conda-forge -c default libarchive -micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #add base only for testing #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ From 7059577b44426749202eea722274be610cf508a2 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 19:33:45 -0400 Subject: [PATCH 056/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 52de77b33..fe6b793fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM mamba-org/micromamba-docker:latest +FROM mambaorg/micromamba:latest # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" From 82ce9c1502b570355d3cbfc48133eeed29934b38 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:36:20 -0400 Subject: [PATCH 057/118] Update Dockerfile --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index fe6b793fe..ee86047a3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,10 +8,10 @@ LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation ARG DEBIAN_FRONTEND=noninteractive # Update Ubuntu Software repository -RUN apt update +#RUN apt update # Install dependencies -RUN apt install -y wget -RUN apt install -y vim +#cRUN apt install -y wget +#cRUN apt install -y vim RUN apt install -y git # Cleanup RUN rm -rf /var/lib/apt/lists/* && \ From 068bec561846aa5696efaaf0fd9409f89f115b7d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:40:52 -0400 Subject: [PATCH 058/118] Update Dockerfile --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index ee86047a3..6dc2ad8a1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,10 +12,10 @@ ARG DEBIAN_FRONTEND=noninteractive # Install dependencies #cRUN apt install -y wget #cRUN apt install -y vim -RUN apt install -y git +#c RUN apt install -y git # Cleanup -RUN rm -rf /var/lib/apt/lists/* && \ - apt clean +#c RUN rm -rf /var/lib/apt/lists/* && \ +#c apt clean # Install Miniconda3 # Download the latest shell script ####RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh From e17805a6fb92ff9bea5d2a1a1550028eb18cae13 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:43:52 -0400 Subject: [PATCH 059/118] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6dc2ad8a1..8142742c5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,8 +26,8 @@ ARG DEBIAN_FRONTEND=noninteractive ####ARG PATH="/root/miniconda3/bin:${PATH}" ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh -RUN conda info -RUN conda init bash +RUN micromamba info +RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics From 7ce98546375e0c92c91f98f3e58bfa9b5f3004e1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:56:46 -0400 Subject: [PATCH 060/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8142742c5..a2dda45e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,7 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info -RUN micromamba init bash +#c RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics From 58a69c6b708f6b1351350bc666ba7e721d9e5beb Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 21:03:10 -0400 Subject: [PATCH 061/118] Update Dockerfile --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index a2dda45e4..b41240afb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -50,4 +50,5 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml # Verify installation RUN /proj/MDTF-diagnostics/mdtf --version # Run mdtf on src/default_tests.jsonc -CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] +# CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] +CMD ["/proj/MDTF-diagnostics/mdtf", "-f","/proj/MDTF-diagnostics/src/default_tests.jsonc"] From b4bcd007962b35dda1d88ed0427458f5e0a529b2 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 21:07:49 -0400 Subject: [PATCH 062/118] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index b41240afb..a10a9248d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -48,7 +48,7 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ #c --env_dir ${CONDA_ENV_DIR} # Verify installation -RUN /proj/MDTF-diagnostics/mdtf --version +RUN /proj/MDTF-diagnostics/mdtf_framework --version # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -CMD ["/proj/MDTF-diagnostics/mdtf", "-f","/proj/MDTF-diagnostics/src/default_tests.jsonc"] +CMD ["/proj/MDTF-diagnostics/mdtf_framework", "--version"] From c469dd3e3b9900514ad5496c4750176216d2f614 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 21:15:59 -0400 Subject: [PATCH 063/118] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index a10a9248d..53e2aecf5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -48,7 +48,7 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ #c --env_dir ${CONDA_ENV_DIR} # Verify installation -RUN /proj/MDTF-diagnostics/mdtf_framework --version +RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -CMD ["/proj/MDTF-diagnostics/mdtf_framework", "--version"] +CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From a9b74d0c28a600751144befe774d44a68a66f9bf Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 09:39:09 -0400 Subject: [PATCH 064/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 53e2aecf5..868e815b0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -43,7 +43,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs #what-really RUN conda install -c conda-forge -c default libarchive RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml - +RUN micromamba activate _MDTF_base #add base only for testing #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ #c --env_dir ${CONDA_ENV_DIR} From 102c68794e3836de135788a200528c5b76d8dc32 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 09:50:22 -0400 Subject: [PATCH 065/118] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 868e815b0..b7a7ad84a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,6 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info +RUN eval "$(micromamba shell hook --shell ) #c RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image From 78d8ce5109d63c3b91ae513d708110031f5c28d7 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 09:52:54 -0400 Subject: [PATCH 066/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b7a7ad84a..e7d2a219f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,7 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info -RUN eval "$(micromamba shell hook --shell ) +RUN eval "$(micromamba shell hook --shell )" #c RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image From a5286cda0dad2a918ec9c07d64f9a3954b8b1128 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:08:40 -0400 Subject: [PATCH 067/118] Update Dockerfile --- Dockerfile | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index e7d2a219f..e389c98c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,9 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info -RUN eval "$(micromamba shell hook --shell )" -#c RUN micromamba init bash -##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge +RUN micromamba shell hook --shell bash # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src From cea4cef755cf08862701fa04e8a4a6a823a72b25 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:17:50 -0400 Subject: [PATCH 068/118] Update Dockerfile --- Dockerfile | 26 ++------------------------ 1 file changed, 2 insertions(+), 24 deletions(-) diff --git a/Dockerfile b/Dockerfile index e389c98c4..5a71d2b7e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,25 +7,6 @@ LABEL version="alpha-01" LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation ARG DEBIAN_FRONTEND=noninteractive -# Update Ubuntu Software repository -#RUN apt update -# Install dependencies -#cRUN apt install -y wget -#cRUN apt install -y vim -#c RUN apt install -y git -# Cleanup -#c RUN rm -rf /var/lib/apt/lists/* && \ -#c apt clean -# Install Miniconda3 -# Download the latest shell script -####RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -#### Change permission to execute build script -####RUN chmod +x Miniconda3-latest-Linux-x86_64.sh -#### Run miniconda installation script -####ENV PATH="/root/miniconda3/bin:${PATH}" -####ARG PATH="/root/miniconda3/bin:${PATH}" -####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b -####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info RUN micromamba shell hook --shell bash # Copy the MDTF-diagnostics package contents from local machine to image @@ -40,14 +21,11 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -#what-really RUN conda install -c conda-forge -c default libarchive RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml -RUN micromamba activate _MDTF_base -#add base only for testing -#c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ -#c --env_dir ${CONDA_ENV_DIR} +#cRUN micromamba activate _MDTF_base # Verify installation RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] +ENTRYPOINT ["micromamba shell hook --shell bash","micromamba activate _MDTF_base"] CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From a10e969674dd3ace1172f885ac602e6519b844e5 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:24:46 -0400 Subject: [PATCH 069/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5a71d2b7e..eab8cf723 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,7 @@ ENV CONDA_ENV_DIR=/opt/conda/envs RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation -RUN /proj/MDTF-diagnostics/mdtf_framework.py --help +#RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] ENTRYPOINT ["micromamba shell hook --shell bash","micromamba activate _MDTF_base"] From a573cb346c0b56e163111ea6935d3a8347b3cdd8 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:38:43 -0400 Subject: [PATCH 070/118] Update main.yml --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 08afe9f16..b60094fd0 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -61,7 +61,7 @@ jobs: image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest - name: Deploy Amazon ECS task definition - uses: aws-actions/amazon-ecs-deploy-task-definition@de0132cf8cdedb79975c6d42b77eb7ea193cf28e + uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 with: task-definition: ${{ steps.task-def.outputs.task-definition }} service: ${{ env.ECS_SERVICE }} From d6d8cfea525c0b6f06e45e212fcd489df6d62d9f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:41:01 -0400 Subject: [PATCH 071/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index eab8cf723..639e32a0c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,5 +27,5 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -ENTRYPOINT ["micromamba shell hook --shell bash","micromamba activate _MDTF_base"] +ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From 6ade7bcd236a07e1cd3eae40c7411188be260e92 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Mon, 28 Aug 2023 18:31:04 -0400 Subject: [PATCH 072/118] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 639e32a0c..c974de3d9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,5 +27,5 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] -CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] +#later ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] +#later CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From ba5b4e3996110b679892142f21e2e77a5d832fca Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Mon, 28 Aug 2023 18:52:18 -0400 Subject: [PATCH 073/118] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index c974de3d9..07e479120 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,7 @@ # Base OS FROM ubuntu:latest FROM mambaorg/micromamba:latest +USER root # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" From ed09195a7c334d4899771dbdb0ab9a847a8db9e3 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 10:27:11 -0400 Subject: [PATCH 074/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 07e479120..824483d41 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,7 +22,7 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help From f59a3cca86afa8e18ab69e1ed08d147e8b97590a Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 10:37:28 -0400 Subject: [PATCH 075/118] Update Dockerfile --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 824483d41..1f6f8742b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,11 +22,11 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -#later ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] -#later CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] +ENTRYPOINT ["micromamba activate _MDTF_base"] +CMD ["/bin/bash", "--help"] From ae547eacdadca8e3e122f74edb123985243a074b Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 11:29:44 -0400 Subject: [PATCH 076/118] Update Dockerfile --- Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1f6f8742b..138fc579c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,11 +22,12 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs +USER mambauser RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -ENTRYPOINT ["micromamba activate _MDTF_base"] -CMD ["/bin/bash", "--help"] +#ENTRYPOINT ["micromamba activate _MDTF_base"] +CMD ["/bin/bash"] From a12ce61040cb1d8b89a39cbaf840178c53ce266d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 11:59:00 -0400 Subject: [PATCH 077/118] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 138fc579c..52178585f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,6 +24,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs USER mambauser RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN export PATH="/proj/MDTF-diagnostics/:$PATH" #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help From ff3e22d2d8f0d211dcd6a16117ddb5dfbda922f4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:42:40 -0400 Subject: [PATCH 078/118] Create docker-build-push-to-cloud.yml --- .github/docker-build-push-to-cloud.yml | 69 ++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 .github/docker-build-push-to-cloud.yml diff --git a/.github/docker-build-push-to-cloud.yml b/.github/docker-build-push-to-cloud.yml new file mode 100644 index 000000000..b60094fd0 --- /dev/null +++ b/.github/docker-build-push-to-cloud.yml @@ -0,0 +1,69 @@ +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Deploy to ECS. Build, push image, + +on: + pull_request: + branches: + - main + +env: + AWS_REGION: us-east-1 # set this to your preferred AWS region, e.g. us-west-1 + ECR_REPOSITORY: mdtf/mdtf-test # set this to your Amazon ECR repository name + ECS_SERVICE: custom-service # MY_ECS_SERVICE set this to your Amazon ECS service name + ECS_CLUSTER: mdtf-east1 # MY_ECS_CLUSTER set this to your Amazon ECS cluster name + ECS_TASK_DEFINITION: ecs-task-defn.json # set this to the path to your Amazon ECS task definition + # file, e.g. .aws/task-definition.json + CONTAINER_NAME: mdtf-test-a1r # set this to the name of the container in the + # containerDefinitions section of your task definition MY_CONTAINER_NAME + +jobs: + deploy: + name: push-to-public-ecr-cache-test + runs-on: ubuntu-latest + environment: dev + + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@13d241b293754004c80624b5567555c4a39ffbe3 + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: ${{ env.AWS_REGION }} + + - name: Build, tag, and push image to Amazon ECR + id: build-image + uses: aradhakrishnanGFDL/docker-build-with-cache-action@master #support-aws-ecr-public + env: + ECR_REGISTRY: public.ecr.aws + IMAGE_TAG: "latest" + ECS_IMAGE: $ECR_REGISTRY/ECR_REPOSITORY:$env.IMAGE_TAG + with: + registry: public.ecr.aws + username: "${{ secrets.AWS_ACCESS_KEY_ID }}" + password: "${{ secrets.AWS_SECRET_ACCESS_KEY }}" + image_name: c6h4h4s8/mdtf/mdtf-test + push_image_and_stages: true + image_tag: latest + + - name: Fill in the new image ID in the Amazon ECS task definition + id: task-def + uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a + with: + task-definition: ${{ env.ECS_TASK_DEFINITION }} + container-name: ${{ env.CONTAINER_NAME }} + image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest + + - name: Deploy Amazon ECS task definition + uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 + with: + task-definition: ${{ steps.task-def.outputs.task-definition }} + service: ${{ env.ECS_SERVICE }} + cluster: ${{ env.ECS_CLUSTER }} + wait-for-service-stability: true From 17d298b3a6422bd0f618c295613c14a145bb072f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:47:22 -0400 Subject: [PATCH 079/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 52178585f..63a7a1d5e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs USER mambauser RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml -RUN export PATH="/proj/MDTF-diagnostics/:$PATH" +ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help From 72d237c451d9586b293ee4b0681db818bf32d73d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:54:38 -0400 Subject: [PATCH 080/118] Delete docker-build-push-to-cloud.yml --- .github/docker-build-push-to-cloud.yml | 69 -------------------------- 1 file changed, 69 deletions(-) delete mode 100644 .github/docker-build-push-to-cloud.yml diff --git a/.github/docker-build-push-to-cloud.yml b/.github/docker-build-push-to-cloud.yml deleted file mode 100644 index b60094fd0..000000000 --- a/.github/docker-build-push-to-cloud.yml +++ /dev/null @@ -1,69 +0,0 @@ -# This workflow uses actions that are not certified by GitHub. -# They are provided by a third-party and are governed by -# separate terms of service, privacy policy, and support -# documentation. - -name: Deploy to ECS. Build, push image, - -on: - pull_request: - branches: - - main - -env: - AWS_REGION: us-east-1 # set this to your preferred AWS region, e.g. us-west-1 - ECR_REPOSITORY: mdtf/mdtf-test # set this to your Amazon ECR repository name - ECS_SERVICE: custom-service # MY_ECS_SERVICE set this to your Amazon ECS service name - ECS_CLUSTER: mdtf-east1 # MY_ECS_CLUSTER set this to your Amazon ECS cluster name - ECS_TASK_DEFINITION: ecs-task-defn.json # set this to the path to your Amazon ECS task definition - # file, e.g. .aws/task-definition.json - CONTAINER_NAME: mdtf-test-a1r # set this to the name of the container in the - # containerDefinitions section of your task definition MY_CONTAINER_NAME - -jobs: - deploy: - name: push-to-public-ecr-cache-test - runs-on: ubuntu-latest - environment: dev - - steps: - - name: Checkout - uses: actions/checkout@v2 - - - name: Configure AWS credentials - uses: aws-actions/configure-aws-credentials@13d241b293754004c80624b5567555c4a39ffbe3 - with: - aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} - aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} - aws-region: ${{ env.AWS_REGION }} - - - name: Build, tag, and push image to Amazon ECR - id: build-image - uses: aradhakrishnanGFDL/docker-build-with-cache-action@master #support-aws-ecr-public - env: - ECR_REGISTRY: public.ecr.aws - IMAGE_TAG: "latest" - ECS_IMAGE: $ECR_REGISTRY/ECR_REPOSITORY:$env.IMAGE_TAG - with: - registry: public.ecr.aws - username: "${{ secrets.AWS_ACCESS_KEY_ID }}" - password: "${{ secrets.AWS_SECRET_ACCESS_KEY }}" - image_name: c6h4h4s8/mdtf/mdtf-test - push_image_and_stages: true - image_tag: latest - - - name: Fill in the new image ID in the Amazon ECS task definition - id: task-def - uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a - with: - task-definition: ${{ env.ECS_TASK_DEFINITION }} - container-name: ${{ env.CONTAINER_NAME }} - image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest - - - name: Deploy Amazon ECS task definition - uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 - with: - task-definition: ${{ steps.task-def.outputs.task-definition }} - service: ${{ env.ECS_SERVICE }} - cluster: ${{ env.ECS_CLUSTER }} - wait-for-service-stability: true From 7399c16ffa70797c9efc0f3f3de920a721a0388b Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:55:34 -0400 Subject: [PATCH 081/118] Create docker-build-push-aws.yml minus the ECR deployment step --- .github/workflows/docker-build-push-aws.yml | 69 +++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 .github/workflows/docker-build-push-aws.yml diff --git a/.github/workflows/docker-build-push-aws.yml b/.github/workflows/docker-build-push-aws.yml new file mode 100644 index 000000000..b60094fd0 --- /dev/null +++ b/.github/workflows/docker-build-push-aws.yml @@ -0,0 +1,69 @@ +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Deploy to ECS. Build, push image, + +on: + pull_request: + branches: + - main + +env: + AWS_REGION: us-east-1 # set this to your preferred AWS region, e.g. us-west-1 + ECR_REPOSITORY: mdtf/mdtf-test # set this to your Amazon ECR repository name + ECS_SERVICE: custom-service # MY_ECS_SERVICE set this to your Amazon ECS service name + ECS_CLUSTER: mdtf-east1 # MY_ECS_CLUSTER set this to your Amazon ECS cluster name + ECS_TASK_DEFINITION: ecs-task-defn.json # set this to the path to your Amazon ECS task definition + # file, e.g. .aws/task-definition.json + CONTAINER_NAME: mdtf-test-a1r # set this to the name of the container in the + # containerDefinitions section of your task definition MY_CONTAINER_NAME + +jobs: + deploy: + name: push-to-public-ecr-cache-test + runs-on: ubuntu-latest + environment: dev + + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@13d241b293754004c80624b5567555c4a39ffbe3 + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: ${{ env.AWS_REGION }} + + - name: Build, tag, and push image to Amazon ECR + id: build-image + uses: aradhakrishnanGFDL/docker-build-with-cache-action@master #support-aws-ecr-public + env: + ECR_REGISTRY: public.ecr.aws + IMAGE_TAG: "latest" + ECS_IMAGE: $ECR_REGISTRY/ECR_REPOSITORY:$env.IMAGE_TAG + with: + registry: public.ecr.aws + username: "${{ secrets.AWS_ACCESS_KEY_ID }}" + password: "${{ secrets.AWS_SECRET_ACCESS_KEY }}" + image_name: c6h4h4s8/mdtf/mdtf-test + push_image_and_stages: true + image_tag: latest + + - name: Fill in the new image ID in the Amazon ECS task definition + id: task-def + uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a + with: + task-definition: ${{ env.ECS_TASK_DEFINITION }} + container-name: ${{ env.CONTAINER_NAME }} + image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest + + - name: Deploy Amazon ECS task definition + uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 + with: + task-definition: ${{ steps.task-def.outputs.task-definition }} + service: ${{ env.ECS_SERVICE }} + cluster: ${{ env.ECS_CLUSTER }} + wait-for-service-stability: true From e894826855caced5c1199735af8eaf28116f008f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:00:57 -0400 Subject: [PATCH 082/118] Create docker-run-test.yml --- .github/workflows/docker-run-test.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .github/workflows/docker-run-test.yml diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml new file mode 100644 index 000000000..6eaf2b9cc --- /dev/null +++ b/.github/workflows/docker-run-test.yml @@ -0,0 +1,15 @@ +name: CI +on: + push: + branches: [ aradhakrishnanGFDL-patch5 ] +jobs: + container-test-job: + runs-on: ubuntu-latest + container: + image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest + env: + NODE_ENV: development + options: --cpus 1 + steps: + - name: Check PATH + run: (echo $PATH) || (echo "No path") From 69c5b3aef059e3f4eff6177d7e0438900824326e Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:03:26 -0400 Subject: [PATCH 083/118] Update docker-build-push-aws.yml --- .github/workflows/docker-build-push-aws.yml | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/.github/workflows/docker-build-push-aws.yml b/.github/workflows/docker-build-push-aws.yml index b60094fd0..8976d9908 100644 --- a/.github/workflows/docker-build-push-aws.yml +++ b/.github/workflows/docker-build-push-aws.yml @@ -3,7 +3,7 @@ # separate terms of service, privacy policy, and support # documentation. -name: Deploy to ECS. Build, push image, +name: Build and push image to Amazon ECR on: pull_request: @@ -51,19 +51,3 @@ jobs: image_name: c6h4h4s8/mdtf/mdtf-test push_image_and_stages: true image_tag: latest - - - name: Fill in the new image ID in the Amazon ECS task definition - id: task-def - uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a - with: - task-definition: ${{ env.ECS_TASK_DEFINITION }} - container-name: ${{ env.CONTAINER_NAME }} - image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest - - - name: Deploy Amazon ECS task definition - uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 - with: - task-definition: ${{ steps.task-def.outputs.task-definition }} - service: ${{ env.ECS_SERVICE }} - cluster: ${{ env.ECS_CLUSTER }} - wait-for-service-stability: true From d4890eadc9b2fda3c8917881273edd6811d3dba1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:06:22 -0400 Subject: [PATCH 084/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 6eaf2b9cc..e748e3245 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -1,7 +1,7 @@ -name: CI +name: docker-run-minitest on: - push: - branches: [ aradhakrishnanGFDL-patch5 ] + pull_request: + branches: [ main ] jobs: container-test-job: runs-on: ubuntu-latest From 13b503d90da86ce7bb32fd095bbd16b438466856 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:17:50 -0400 Subject: [PATCH 085/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index e748e3245..5e0580268 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -13,3 +13,7 @@ jobs: steps: - name: Check PATH run: (echo $PATH) || (echo "No path") + - name: Activate environment + run: (micromamba activate _MDTF_base) || (echo "Unable to activate environment") + - name: Get version of mdtf_framework.py + run: (mdtf_framework.py --version) From 31218a0683570fc34a0d061eaf5f3aad5ff90f48 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:27:19 -0400 Subject: [PATCH 086/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 5e0580268..4856418ff 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba activate _MDTF_base) || (echo "Unable to activate environment") + run: (eval "$(micromamba shell hook --shell )" + micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 060efab5e714213baa005b328912b95bb3f38c91 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:28:59 -0400 Subject: [PATCH 087/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 4856418ff..3eed90770 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (eval "$(micromamba shell hook --shell )" + run: (eval "$(micromamba shell hook --shell bash)" micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 65c4fa8c8251335b561a51e8eea338b7c9ff8dfc Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:31:35 -0400 Subject: [PATCH 088/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 3eed90770..0ada44cb7 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (eval "$(micromamba shell hook --shell bash)" - micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook --shell bash))" + micromamba activate _MDTF_base - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 225a0ab1733f3e63a94ed0d413303fffdcb85b3c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:35:27 -0400 Subject: [PATCH 089/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 0ada44cb7..e4205fb06 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -13,8 +13,9 @@ jobs: steps: - name: Check PATH run: (echo $PATH) || (echo "No path") - - name: Activate environment + - name: Shell init for micromamba run: (eval "$(micromamba shell hook --shell bash))" + - name: Activate environment micromamba activate _MDTF_base - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 6b5a7dc016ecabf8e48382f883852807530862fb Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:38:19 -0400 Subject: [PATCH 090/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index e4205fb06..e0cbed4b9 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -16,6 +16,6 @@ jobs: - name: Shell init for micromamba run: (eval "$(micromamba shell hook --shell bash))" - name: Activate environment - micromamba activate _MDTF_base + run: (micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py - run: (mdtf_framework.py --version) + run: (mdtf_framework.py --version) From 542e6fc50f6cb0e7cd615966974bca7216ae7b1c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:32:18 -0400 Subject: [PATCH 091/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index e0cbed4b9..2ae85cc9f 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Shell init for micromamba - run: (eval "$(micromamba shell hook --shell bash))" + run: (eval "$(micromamba shell hook --shell bash)") - name: Activate environment run: (micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py From 2556a392a6a1d93451401ceacce576ee77cf1ce4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:35:34 -0400 Subject: [PATCH 092/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 2ae85cc9f..0bf0564f6 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Shell init for micromamba - run: (eval "$(micromamba shell hook --shell bash)") + run: (micromamba shell hook --shell bash) - name: Activate environment run: (micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py From 3756eac88f9cb262c505df4f40f58bd60685b2fa Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:45:07 -0400 Subject: [PATCH 093/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 0bf0564f6..2cc3acac5 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -16,6 +16,6 @@ jobs: - name: Shell init for micromamba run: (micromamba shell hook --shell bash) - name: Activate environment - run: (micromamba activate _MDTF_base) + run: (micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 74acf422e68e5d1c5b0ff5dac02f7e857d75d732 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:47:32 -0400 Subject: [PATCH 094/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 2cc3acac5..f758a4f43 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -13,9 +13,7 @@ jobs: steps: - name: Check PATH run: (echo $PATH) || (echo "No path") - - name: Shell init for micromamba - run: (micromamba shell hook --shell bash) - name: Activate environment - run: (micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell hook --shell bash; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 437c175153384074f2e049b94c37c31dc09c6979 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:53:32 -0400 Subject: [PATCH 095/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index f758a4f43..2f5fd8d8b 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell hook --shell bash; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From bb7fc1fd1723bf7675ceb5c3686f3c7b65385886 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 15:39:47 -0400 Subject: [PATCH 096/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 2f5fd8d8b..edaa45656 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell bash --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 576070a38b0bf519fd40b46c1f32fc95a0435f90 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 15:47:06 -0400 Subject: [PATCH 097/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index edaa45656..129ac99e4 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell bash --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 96f398cdf799ee04020a83e1c0458036df3b4c36 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 21:10:30 -0400 Subject: [PATCH 098/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 129ac99e4..1e314ca17 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell=bash; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; source ~/.bashrc; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From aef473c3cea0247f4655fb987ead76b1b951ed27 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 21:18:59 -0400 Subject: [PATCH 099/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 1e314ca17..c367979d4 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell=bash; source ~/.bashrc; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 73b2f10667f93b8daff0a2cb01b883af8feb4963 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 16:45:08 -0400 Subject: [PATCH 100/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c367979d4..959540718 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -11,9 +11,15 @@ jobs: NODE_ENV: development options: --cpus 1 steps: - - name: Check PATH - run: (echo $PATH) || (echo "No path") + - uses: mamba-org/setup-micromamba@v1 + with: + micromamba-version: '1.3.1-0' + init-shell: >- + bash + powershell + cache-environment: true + post-cleanup: 'all' - name: Activate environment - run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 325a87b6512623f67ea70a3de56c01441a47224f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 16:47:12 -0400 Subject: [PATCH 101/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 959540718..a29caeb60 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -17,7 +17,6 @@ jobs: init-shell: >- bash powershell - cache-environment: true post-cleanup: 'all' - name: Activate environment run: (micromamba activate; micromamba activate _MDTF_base) From c2f5de60c21b7e8388ae0b3ffe3088cb7349a3fc Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:00:59 -0400 Subject: [PATCH 102/118] Update Dockerfile --- Dockerfile | 47 +++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 43 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 63a7a1d5e..99637024d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,15 +1,53 @@ # Base OS FROM ubuntu:latest FROM mambaorg/micromamba:latest + +#micromamba set up + USER root + +# if your image defaults to a non-root user, then you may want to make the +# next 3 ARG commands match the values in your image. You can get the values +# by running: docker run --rm -it my/image id -a +ARG MAMBA_USER=mambauser +ARG MAMBA_USER_ID=57439 +ARG MAMBA_USER_GID=57439 +ENV MAMBA_USER=$MAMBA_USER +ENV MAMBA_ROOT_PREFIX="/opt/conda" +ENV MAMBA_EXE="/bin/micromamba" + +COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" +COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh +COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh +COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh +COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh +COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh + +RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ + /usr/local/bin/_dockerfile_setup_root_prefix.sh + +USER $MAMBA_USER + +SHELL ["/usr/local/bin/_dockerfile_shell.sh"] + +ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] +# Optional: if you want to customize the ENTRYPOINT and have a conda +# environment activated, then do this: +# ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "my_entrypoint_program"] + +RUN micromamba info +RUN micromamba shell hook --shell bash +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + +## + # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation ARG DEBIAN_FRONTEND=noninteractive -RUN micromamba info -RUN micromamba shell hook --shell bash + # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src @@ -22,8 +60,9 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -USER mambauser -RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + +#USER mambauser +#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base # Verify installation From d8c08d1a2a03410e8b63055f1bee3ed0e7773736 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:02:01 -0400 Subject: [PATCH 103/118] Update docker-build-push-aws.yml --- .github/workflows/docker-build-push-aws.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-build-push-aws.yml b/.github/workflows/docker-build-push-aws.yml index 8976d9908..3f400a384 100644 --- a/.github/workflows/docker-build-push-aws.yml +++ b/.github/workflows/docker-build-push-aws.yml @@ -3,7 +3,7 @@ # separate terms of service, privacy policy, and support # documentation. -name: Build and push image to Amazon ECR +name: Build and push image to Amazon ECR. on: pull_request: From eca019da68b70ce20fa9e1f95d50654d7e172acf Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:05:12 -0400 Subject: [PATCH 104/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index a29caeb60..c367979d4 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -11,14 +11,9 @@ jobs: NODE_ENV: development options: --cpus 1 steps: - - uses: mamba-org/setup-micromamba@v1 - with: - micromamba-version: '1.3.1-0' - init-shell: >- - bash - powershell - post-cleanup: 'all' + - name: Check PATH + run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 33a59a5364bcb2225cda3875814e894a686ea917 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:11:24 -0400 Subject: [PATCH 105/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 99637024d..d68cd2f55 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM mambaorg/micromamba:latest +FROM mambaorg/micromamba:1.5.0 as micromamba #micromamba set up From dc8dab268f3a7fd50bcf34c41e16793bb0da8c6d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:12:01 -0400 Subject: [PATCH 106/118] Update Dockerfile --- Dockerfile | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index d68cd2f55..29b09f8b9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,8 +8,9 @@ USER root # if your image defaults to a non-root user, then you may want to make the # next 3 ARG commands match the values in your image. You can get the values -# by running: docker run --rm -it my/image id -a -ARG MAMBA_USER=mambauser +# by running: docker run --rm -it my/image id -a + +ARG MAMBA_USER=mambauser ARG MAMBA_USER_ID=57439 ARG MAMBA_USER_GID=57439 ENV MAMBA_USER=$MAMBA_USER @@ -28,6 +29,7 @@ RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ USER $MAMBA_USER + SHELL ["/usr/local/bin/_dockerfile_shell.sh"] ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] @@ -36,6 +38,8 @@ ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] # ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "my_entrypoint_program"] RUN micromamba info +RUN "echo done" + RUN micromamba shell hook --shell bash RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml @@ -46,7 +50,7 @@ LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation -ARG DEBIAN_FRONTEND=noninteractive +#ARG DEBIAN_FRONTEND=noninteractive # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics @@ -63,6 +67,7 @@ ENV CONDA_ENV_DIR=/opt/conda/envs #USER mambauser #RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base # Verify installation From 5ba6cfd2459a9cc50339e4f69ee029e24829d6b4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:13:06 -0400 Subject: [PATCH 107/118] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 29b09f8b9..0d82f1fd5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM mambaorg/micromamba:1.5.0 as micromamba +FROM mambaorg/micromamba:latest as micromamba #micromamba set up From 8498b796ba08612dd33c0dd1b3dfb3546b723804 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:14:29 -0400 Subject: [PATCH 108/118] Update Dockerfile --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index 0d82f1fd5..da1694b04 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,6 +17,8 @@ ENV MAMBA_USER=$MAMBA_USER ENV MAMBA_ROOT_PREFIX="/opt/conda" ENV MAMBA_EXE="/bin/micromamba" +######### + COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh From b118a1b96f698826f86eade79ce9039c5b824806 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:26:10 -0400 Subject: [PATCH 109/118] Update Dockerfile --- Dockerfile | 36 ++---------------------------------- 1 file changed, 2 insertions(+), 34 deletions(-) diff --git a/Dockerfile b/Dockerfile index da1694b04..048f6bf57 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,38 +6,7 @@ FROM mambaorg/micromamba:latest as micromamba USER root -# if your image defaults to a non-root user, then you may want to make the -# next 3 ARG commands match the values in your image. You can get the values -# by running: docker run --rm -it my/image id -a - -ARG MAMBA_USER=mambauser -ARG MAMBA_USER_ID=57439 -ARG MAMBA_USER_GID=57439 -ENV MAMBA_USER=$MAMBA_USER -ENV MAMBA_ROOT_PREFIX="/opt/conda" -ENV MAMBA_EXE="/bin/micromamba" - -######### - -COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" -COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh -COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh - -RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ - /usr/local/bin/_dockerfile_setup_root_prefix.sh - -USER $MAMBA_USER - - -SHELL ["/usr/local/bin/_dockerfile_shell.sh"] - -ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] -# Optional: if you want to customize the ENTRYPOINT and have a conda -# environment activated, then do this: -# ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "my_entrypoint_program"] +USER $MAMBA_USER RUN micromamba info RUN "echo done" @@ -46,7 +15,6 @@ RUN micromamba shell hook --shell bash RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ## - # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" @@ -56,7 +24,7 @@ LABEL description="This is a docker image for the MDTF-diagnostics package" # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics -COPY src ${CODE_ROOT}/src +COPY src ${CODE_ROOT}/src COPY data ${CODE_ROOT}/data #COPY diagnostics ${CODE_ROOT}/diagnostics COPY mdtf_framework.py ${CODE_ROOT} From af8d669df83028222184ff76f903f4ed9f9671d8 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 20:41:53 -0400 Subject: [PATCH 110/118] Update Dockerfile --- Dockerfile | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 048f6bf57..a8e4ecead 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,10 +6,8 @@ FROM mambaorg/micromamba:latest as micromamba USER root -USER $MAMBA_USER - RUN micromamba info -RUN "echo done" + RUN micromamba shell hook --shell bash RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml From c3edd04553389e52b6492ba667c24ae8771c27e5 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 20:46:25 -0400 Subject: [PATCH 111/118] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index a8e4ecead..f0db5afac 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,7 +10,7 @@ RUN micromamba info RUN micromamba shell hook --shell bash -RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ## # Container Metadata @@ -34,7 +34,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs #USER mambauser -#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base From 4fd92fe70796c60bcf8c5660fdc198241da399f3 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:02:40 -0400 Subject: [PATCH 112/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c367979d4..433ff5594 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -1,4 +1,4 @@ -name: docker-run-minitest +name: docker-run-minitest1 on: pull_request: branches: [ main ] From 7e0bffec9c2e12ab711d66dd1215bb6f46fd5ca2 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:04:11 -0400 Subject: [PATCH 113/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 433ff5594..b314ca799 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 1a5687f5df249e9c4e1cb307073ebb8e361a4dee Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:15:29 -0400 Subject: [PATCH 114/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index b314ca799..c7578c5f0 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba activate; micromamba activate _MDTF_base) + shell: bash + run: (micromamba shell hook -s bash -p ~/conda; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 618ae853e70aed6b6721401922b9a944602a9776 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:20:02 -0400 Subject: [PATCH 115/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c7578c5f0..c425cb78a 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -15,6 +15,6 @@ jobs: run: (echo $PATH) || (echo "No path") - name: Activate environment shell: bash - run: (micromamba shell hook -s bash -p ~/conda; micromamba activate; micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook -s bash -p ~/conda); micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From e0ee8e1f1386263a466b7f4fa42b0443145dc253 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:25:46 -0400 Subject: [PATCH 116/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c425cb78a..b656beeb5 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -15,6 +15,6 @@ jobs: run: (echo $PATH) || (echo "No path") - name: Activate environment shell: bash - run: (eval "$(micromamba shell hook -s bash -p ~/conda); micromamba activate; micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From aee3f551ee4973a0a39e7db343add38b2b57d1ae Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:32:37 -0400 Subject: [PATCH 117/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index b656beeb5..381362187 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -15,6 +15,6 @@ jobs: run: (echo $PATH) || (echo "No path") - name: Activate environment shell: bash - run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base;mdtf_framework.py --version) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 2701f37ad3ed3f92dc8af6a5c334f3ccfe42d7b1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:35:15 -0400 Subject: [PATCH 118/118] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 381362187..dfddcb24c 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -16,5 +16,3 @@ jobs: - name: Activate environment shell: bash run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base;mdtf_framework.py --version) - - name: Get version of mdtf_framework.py - run: (mdtf_framework.py --version)