Merge branch 'main' of https://github.com/BenWinchester/PVTModel

.gitattributes

@@ -0,0 +1,4 @@
+# Set line endings to be LF rather than CRLF.
+*.py text eol=lf
+*.txt text eol=lf
+*.yaml text eol=lf

CITATION.cff

@@ -0,0 +1,18 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Winchester
+    given-names: Benedict
+    orcid: https://orcid.org/0000-0002-2880-1243
+  - family-names: Huang
+    given-names: Gan
+  - family-names: Nelson
+    given-names: Jenny
+    orcid: https://orcid.org/0000-0003-1048-1330
+  - family-names: Markides
+    given-names: Christos N.
+    orcid: https://orcid.org/0000-0002-4219-1867
+title: HEATPanel
+version: v1.1
+date-released: 2022-09-13
+url: "https://github.com/BenWinchester/PVTModel"

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement by containg the
+developers directly.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

@@ -0,0 +1,134 @@
+# Contributing to PVTModel
+
+:+1::tada: First off, thanks for taking the time to contribute! :tada::+1:
+
+The following is a set of guidelines for contributing to PVTModel, the repository associated with the `heat-panel` Python package. These guidelines are hosted on GitHub and are maintained, so ensure you have the latest version via a `git pull`. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
+
+#### Table Of Contents
+
+[Code of Conduct](#code-of-conduct)
+
+[What should I know before I get started?](#what-should-i-know-before-i-get-started)
+  * [What is PVTModel for?](#what-is-pvtmodel-for)
+  * [What is PVTModel not for?](#what-is-pvtmodel-not-for)
+
+[How to contribute to PVTModel](#how-to-contribute-to-PVTModel)
+  * [Reporting bugs](#reporting-bugs)
+  * [Merging patches](#merging-patches)
+    * [Cosmetic patches](#cosmetic-patches)
+  * [Questions](#questions)
+
+[Styleguides](#styleguides)
+  * [Git commit messages](#git-commit-messages)
+  * [Python styleguide](#python-styleguide)
+  * [YAML styleguide](#yaml-styleguide)
+  * [Changing styleguides](#changing-styleguides)
+
+
+### Code of Conduct
+
+This project and everyone participating in it is governed by the [PVTModel Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to @BenWinchester.
+
+### What should I know before I get started?
+
+PVTModel was developed at Imperial College London as a means of simulating the electrical and thermal characteristics of hybrid photovoltaic-thermal collectors. The name, `HEATPanel`, refers to this: Hybrid Electricity And Thermal Panel. Primarilly, sheet-and-tube collectors have been investigated, and default data for these panels is provided which can be adjusted by the user.
+
+PVTModel has the capability to model these panels in a great level of detail, considering layer- and element-wise thermal and electrical characteristics. These are then aggregated to provide overall performance features which are useful when considering these types of collectors.
+
+#### What is PVTModel for?
+
+PVTModel is a software tool for simulating the electrical and thermal characteristics of hybrid PV-T collectors, specifically sheet-and-tube collectors, though support for more collectors is being developed as part of the ongoing process of expanding the functionality of the software package. These collectors can be considered as part of a wider hot-water demand system, including storage tanks and heat exchangers, or as standalone collectors under test conditions. 2D temperature maps of each layer can be generated for vieweing the collectors' thermal properties.
+
+#### What is PVTModel not for?
+
+Fundamentally, PVTModel is a matrix solver with bells and whistles added to ensure a user-friendly process for seamlessly adjusting parameters without having to recreate a matrix equation manually for each calculation that a user could wish to solve. With this in mind, chosing parameters that are outside a standard scope of a matrix solver may lead to divergent solutions.
+
+PVTModel is also currently only developed for sheet-and-tube PV-T collectors. This is a great limitation in terms of the available market of PV-T collectors which currently exist, and the multitude of designs in development. However, sheet-and-tube collectors are currently the most widely implemented.
+
+## How to contribute to PVTModel
+
+### Reporting bugs
+
+**Did you find a bug?** Bugs make it into the code from time to time. If you spot a bug, report it as follows:
+
+* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/BenWinchester/PVTModel/issues).
+
+* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/BenWinchester/PVTModel/issues/new/choose). 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 the issue is a **bug**, use the [Bug report](BenWinchester/PVTModel/issues/new?assignees=&labels=bug&template=bug_report.md&title=) template,
+
+  * If the issue is a **feature** request for something new that you would like to see introduced into PVTModel, use the [Feature request](BenWinchester/PVTModel/issues/new?assignees=&labels=bug&template=feature_request.md&title=) template.
+
+### Merging patches
+
+**Did you write a patch that fixes a bug?** If you have coded a solution for a bug that you have found or for an open issue, open a pull request for it as follows:
+
+* 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,
+
+  * Follow the template information presented, filling in all the fields requested which are relevant to your patch.
+
+* Ensure that you include at least one administrator reviewer for your pull request. Without an appropriate review, you will be unable to merge your pull request.
+
+#### Cosmetic patches
+
+**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 PVTModel will generally not be accepted. Contact the developers directly, or save your cosmetic changes until you are able to merge them as part of a feature or bug issue.
+
+### Questions
+
+**Do you have questions about the source code?** Ask any question about how to use PVTModel on the [Discussions](https://github.com/BenWinchester/PVTModel/discussions) page.
+
+## Styleguides
+
+### Git commit messages
+
+* Git Commit Messages
+* Use the present tense ("Add feature" not "Added feature")
+* Use the imperative mood ("Move cursor to..." not "Moves cursor to...")
+* Limit the first line to 72 characters or less
+* Reference issues and pull requests liberally after the first line
+* When only changing documentation, include [ci skip] in the commit title
+* Consider starting the commit message with an applicable emoji:
+  * 🎉 `:tada` when adding an initial commit or solving a difficult problem
+  * 🎨 `:art:` when improving the format/structure of the code
+  * 🐎 `:racehorse:` when improving performance
+  * 📝 `:memo:` when writing docs
+  * 🐧 `:penguin:` when fixing something on Linux
+  * ✨ `:sparkles:` when adding a new feature
+  * 🚧 `:construction:` when part-way through working on code
+  * 🍎 `:apple:` when fixing something on macOS
+  * 🏁 `:checkered_flag:` when fixing something on Windows
+  * ⏪ `:rewind:` when backing out a commit or changes
+  * 🐛 `:bug:` when fixing a bug
+  * 🔥 `:fire:` when removing code or files
+  * 💚 `:green_heart:` when fixing the CI build
+  * 👕 `:shirt:` when removing linter warnings
+  * ✅ `:white_check_mark:` when adding tests
+  * 🔒 `:lock:` when dealing with security
+  * ⬆️ `:arrow_up:` when upgrading dependencies
+  * ⬇️ `:arrow_down:` when downgrading dependencies
+  * 🚀 `:rocket:` when deploying code
+
+### Python styleguide
+
+All `Python` code must conform to [mypy](https://github.com/python/mypy) and [pylint](https://github.com/PyCQA/pylint) coding standards and must be formatted with the [black](https://github.com/psf/black) formatter:
+* A `mypy.ini` file within the root of the repository sets out the requirements that must be met by any code. Use `python -m mypy src/` to ensure that your code complies with the guidelines.
+* A `.pylintrc` file within the root of the repository sets out the linting requirements. Use `python -m pylint src/` to ensure that your code complies with the guidelines.
+* All code must be formatted with `black`.
+
+These tests must pass for any pull request to be successfully approved and merged. You can run these tests from the root of the repository with `./bin/test-clover.sh`.
+
+### YAML styleguide
+
+All `.yaml` files which are modified are linted with [yamllint](https://github.com/adrienverge/yamllint). You can use `yamllint -c .yamllint-config.yaml` to run `yamllint` over any `.yaml` files that you have modified.
+
+### Changing styleguides
+
+If you have any changes for the styleguides, make these **very clear** within your pull request message. It is unusual to have to change the styleguides to make your code pass the required tests.
+
+Thanks! :heart: :heart: :heart:
+
+PVTModel Team

README.md

@@ -1,4 +1,4 @@
-# FirstPVTModel
+# HEATPanel
 2D model for a PVT system.
 
 ## Model basics.

bin/hpc_pvt_machine_learning.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+########################################################################################
+# hpc_pvt_machine_learning.sh.py - Runs the machine-learning fitting on the HPC.       #
+#                                                                                      #
+# Author(s): Ben Winchester                                                            #
+# Copyright: Ben Winchester, 2022                                                      #
+# Date created: 30/09/2022                                                             #
+# License: Open source                                                                 #
+# Most recent update: 30/09/2022                                                       #
+#                                                                                      #
+# For more information, please email:                                                  #
+#     [email protected]                                                    #
+########################################################################################
+
+#PBS -lwalltime=72:00:00
+#PBS -lselect=1:ncpus=8:mem=11800Mb
+
+echo -e "HPC script executed."
+# Depending on the environmental variable, run the appropriate HPC job.
+
+module load anaconda3/personal
+source activate py37
+
+OUTPUT_DIR="$PBS_O_WORKDIR"
+CURRENT_DIR=$(pwd)
+cd $PBS_O_WORKDIR
+
+INPUT_FILE="combined_data.json"
+OUTPUT_DIR="machine_learning_outputs"
+
+echo -e "Running machine-learning python program."
+
+python3.7 -u -m src.pvt_model.analysis.machine_learning_fit -cv \
+    -df $INPUT_FILE -f -np 14
+
+cd $CURRENT_DIR
+
+echo -e "Script exectued."
+
+exit 0

src/pvt_model/analysis/machine_learning_fit.py

@@ -121,24 +121,24 @@
 
 # Number of estimators:
 #   Number of trees in random forest
-N_ESTIMATORS = [int(x) for x in np.linspace(start=5, stop=200, num=40)]
+N_ESTIMATORS = [int(x) for x in np.linspace(start=5, stop=1000, num=200)]
 
 # Max features:
 #   Number of features to consider at every split
 MAX_FEATURES: List[str] = ["auto", "sqrt"]
 
 # Max depth:
 #   Maximum number of levels in tree
-MAX_DEPTH: List[Optional[int]] = [int(x) for x in np.linspace(1, 15, num=15)]
+MAX_DEPTH: List[Optional[int]] = [int(x) for x in np.linspace(1, 40, num=40)]
 MAX_DEPTH.append(None)
 
 # Min samples spllit:
 #   Minimum number of samples required to split a node
-MIN_SAMPLES_SPLIT: List[int] = [2, 5, 10, 15, 20, 40]
+MIN_SAMPLES_SPLIT: List[int] = [int(x) for x in np.linspace(5, 100, num=10)]
 
 # Min samples leaf:
 #   Minimum number of samples required at each leaf node
-MIN_SAMPLES_LEAF: List[int] = [1, 2, 4, 8, 15, 30]
+MIN_SAMPLES_LEAF: List[int] = [int(x) for x in np.linspace(1, 100, num=20)]
 
 # Bootstrap:
 #   Method of selecting samples for training each tree
@@ -387,7 +387,6 @@ def _train_trees_and_forest(
             pickle.dump(best_thermal_forest, f)
 
 
-
 def analyse(
     cv_search: bool, data_file_name: str, forest: bool, num_pipes_correction: int, use_existing_fits: bool
 ) -> None: