Merge pull request #453 from xchem/precommit-fixes

Removed files filter on pre-commit config

.gitignore

@@ -131,4 +131,4 @@ ENV/
 # emacs temp files
 *~
 \#*#
-\#*
+\#*

.pre-commit-config.yaml

@@ -1,7 +1,5 @@
 ---
 minimum_pre_commit_version: 3.1.1
-# It's a legacy project and likely to be noisy - limit to key directories...
-files: ^viewer/
 
 repos:
 
@@ -51,14 +49,14 @@ repos:
 # pylint may pass on pre-commit but fail in CI - but at least
 # the user has done 90% of the lint checks before the code
 # hits the server.
-- repo: https://github.com/pycqa/pylint
-  rev: v3.0.2
-  hooks:
-  - id: pylint
-    additional_dependencies:
-    - pylint-django
-    args:
-    - --load-plugins
-    - pylint_django,pylint_django.checkers.migrations
-    - --django-settings-module
-    - fragalysis.settings
+#- repo: https://github.com/pycqa/pylint
+#  rev: v3.0.2
+#  hooks:
+#  - id: pylint
+#    additional_dependencies:
+#    - pylint-django
+#    args:
+#    - --load-plugins
+#    - pylint_django,pylint_django.checkers.migrations
+#    - --django-settings-module
+#    - fragalysis.settings

design_docs/JobSumitterMainFlow.puml

@@ -69,4 +69,4 @@ group Automatic upload (future improvement)
     user -> fb : upload_results
     fb -> user :Computed set details
 end
-@enduml
+@enduml

design_docs/download_structures.md

@@ -1,9 +1,9 @@
 # Download Structures Notes
 
-Firstly, note that everything comes from the aligned path. 
+Firstly, note that everything comes from the aligned path.
 The original plan was for the contents of the zip file to come from the links that are currently stored in the Fragalysis database, so I did the design based on this.
 
-The extra work for the crystalographic path is detailed in https://github.com/m2ms/fragalysis-frontend/issues/673. This needs updating I think based on what we know now. 
+The extra work for the crystalographic path is detailed in https://github.com/m2ms/fragalysis-frontend/issues/673. This needs updating I think based on what we know now.
 
 The mapping for the aligned files stored in the database (the ones we currently output) is as follows:
 

django_nginx.conf

@@ -42,7 +42,7 @@ server {
     location /target_loader_data/ {
         alias /code/media/target_loader_data/;
         internal;
-    }    
+    }
     location / {
         proxy_pass http://unix:/code/django_app.sock;
         uwsgi_read_timeout 1000s;

doc_templates/README.md

@@ -16,29 +16,29 @@ _Download snapshot_:  https://https://fragalysis.xchem.diamond.ac.uk/viewer/reac
 
 ### Download options selected
 (** Note to be added**)
-The following options were checked in the download dialogue: 
+The following options were checked in the download dialogue:
 * Selected: All structures
 * Selected: PanDDA Event maps - primary evidence
 * Selected: Incremental - always up-to-date with latest structures
 * Selected: Single SDF of all ligands
 
 [use actual words in the modal - just type them across if necessary]
 
-### Download command (JSON)   
+### Download command (JSON)  
 JSON command sent from front-end to backend to generate the download.  This can be reused programmatically as a POST command
 
 The actual JSON (**Note: To be updated currently taken from request, but should be taken from front end**)
 
-## Directory structure  [subheading] 
+## Directory structure  [subheading]
 `[The text from download_readme_template.md.]`
 
 ## Files included
 `[Bulleted List of files in zip]`
 
 
- 
+
 - The Download URL
 - The API parameters used
 - A list of the files in the zip file.
 
-The file will then be turned into a PDF before being added to the zip file.
+The file will then be turned into a PDF before being added to the zip file.

docker-entrypoint.sh

@@ -25,7 +25,7 @@ elif [ "${CONTAINER_ROLE,,}" = "stack" ]; then
   /code/launch-stack.sh
 
 else
-  
+
   # Unsupported Role! (this should never happen)
   echo "+> CONTAINER_ROLE is not supported!"
 

docs/build/html/API/api_intro.html

@@ -17,22 +17,22 @@
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Crystallographic data (Models)" href="../crystallographic_data/schema.html" />
     <link rel="prev" title="Running in Production (+CI/CD)" href="../dev_setup/production.html" />
-   
+
   <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-  
-  
+
+
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
-  
+
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          
+
 
           <div class="body" role="main">
-            
+
   <div class="section" id="restful-api-models-serializers-and-views">
 <span id="api-intro"></span><h1>RESTful API (Models, Serializers and Views)<a class="headerlink" href="#restful-api-models-serializers-and-views" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="introduction">
@@ -244,7 +244,7 @@ <h2>EXAMPLE - Model, Serializer, View and URL for Target model<a class="headerli
 
 
           </div>
-          
+
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -314,18 +314,18 @@ <h3 id="searchlabel">Quick search</h3>
     </div>
     <div class="footer">
       &copy;2020, Rachael Skyner.
-      
+
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
-      
+
       |
       <a href="../_sources/API/api_intro.rst.txt"
           rel="nofollow">Page source</a>
     </div>
 
-
 
-
+
+
   </body>
-</html>
+</html>

docs/build/html/API/media.html

@@ -16,22 +16,22 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="prev" title="Uploading computational data (Celery tasks and django template)" href="../computational_data/tasks.html" />
-   
+
   <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-  
-  
+
+
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
-  
+
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          
+
 
           <div class="body" role="main">
-            
+
   <div class="section" id="serving-static-files-media">
 <h1>Serving static files (media)<a class="headerlink" href="#serving-static-files-media" title="Permalink to this headline">¶</a></h1>
 <p>There are some files, such as PDB files, that need to be served by fragalysis. These are either:</p>
@@ -172,7 +172,7 @@ <h2>Adding an endpoint that serves media<a class="headerlink" href="#adding-an-e
 
 
           </div>
-          
+
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -240,18 +240,18 @@ <h3 id="searchlabel">Quick search</h3>
     </div>
     <div class="footer">
       &copy;2020, Rachael Skyner.
-      
+
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
-      
+
       |
       <a href="../_sources/API/media.rst.txt"
           rel="nofollow">Page source</a>
     </div>
 
-
 
-
+
+
   </body>
-</html>
+</html>

docs/build/html/API/misc_views.html

@@ -17,22 +17,22 @@
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Uploading data (Celery tasks and django template)" href="../computational_data/tasks.html" />
     <link rel="prev" title="Project data (Views)" href="../projects/views.html" />
-   
+
   <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-  
-  
+
+
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
-  
+
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
-          
+
 
           <div class="body" role="main">
-            
+
   <div class="section" id="miscellaneous-data">
 <h1>Miscellaneous data<a class="headerlink" href="#miscellaneous-data" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="miscellaneous-views">
@@ -575,7 +575,7 @@ <h2>Tag Views<a class="headerlink" href="#tag-views" title="Permalink to this he
 
 
           </div>
-          
+
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -648,18 +648,18 @@ <h3 id="searchlabel">Quick search</h3>
     </div>
     <div class="footer">
       &copy;2020, Rachael Skyner.
-      
+
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
-      
+
       |
       <a href="../_sources/API/misc_views.rst.txt"
           rel="nofollow">Page source</a>
     </div>
 
-
 
-
+
+
   </body>
-</html>
+</html>

docs/build/html/_sources/API/api_intro.rst.txt

@@ -242,4 +242,4 @@ If we navigate to the URL :code:`<root>/api/targets/?title=<target_name>` we are
 .. image:: target_api.png
 
 This is a page automatically generated by DRF, and includes options to see what kinds of requests you can make against
-this endpoint.
+this endpoint.

docs/build/html/_sources/computational_data/schema.rst.txt

@@ -25,4 +25,4 @@ Model details
 
 .. autoclass:: viewer.models.NumericalScoreValues
 
-.. autoclass:: viewer.models.CSetKeys
+.. autoclass:: viewer.models.CSetKeys

docs/build/html/_sources/computational_data/views.rst.txt

@@ -72,4 +72,3 @@ View details
 
 .. autoclass:: viewer.views.pset_download
     :members:
-

docs/build/html/_sources/crystallographic_data/schema.rst.txt

@@ -22,4 +22,3 @@ Model details
 .. autoclass:: viewer.models.Compound
 
 .. autoclass:: viewer.models.Molecule
-

docs/build/html/_sources/crystallographic_data/views.rst.txt

@@ -72,4 +72,3 @@ View details
 
 .. autoclass:: viewer.views.CompoundImageView
     :members:
-

docs/build/html/_sources/dev_setup/production.rst.txt

@@ -1,4 +1,4 @@
 Running in Production (+CI/CD)
 ==============================
 The fragalysis stack deployment and CI/CD orchestration is described elsewhere:
-https://dls-fragalysis-stack-kubernetes.readthedocs.io/en/latest/index.html
+https://dls-fragalysis-stack-kubernetes.readthedocs.io/en/latest/index.html

docs/build/html/_sources/dev_setup/stack_setup.rst.txt

@@ -190,4 +190,4 @@ Note: **please don't push this change into git**
     popd || exit #etc
 
     # re-run docker compose
-    docker-compose -f docker-compose.dev.yml up
+    docker-compose -f docker-compose.dev.yml up

docs/build/html/_sources/intro.rst.txt

@@ -69,4 +69,4 @@ context described here.
 The Stack
 ---------
 The fragalysis stack is very intentionally split up into many components, each with its own codebase. This documentation
-only covers the backend, as described in the introduction.
+only covers the backend, as described in the introduction.

docs/build/html/_sources/projects/schema.rst.txt

@@ -17,4 +17,4 @@ Model details
 
 .. autoclass:: viewer.models.SessionProject
 
-.. autoclass:: viewer.models.Snapshot
+.. autoclass:: viewer.models.Snapshot

docs/build/html/_static/alabaster.css

@@ -698,4 +698,4 @@ nav#breadcrumbs li+li:before {
     div.related {
         display: none;
     }
-}
+}

docs/build/html/_static/basic.css

@@ -760,4 +760,4 @@ div.math:hover a.headerlink {
     #top-link {
         display: none;
     }
-}
+}

docs/build/html/_static/css/functions.css

@@ -14,4 +14,4 @@
     border-bottom: 1px solid #dadeff;
     padding-bottom: 5px;
     padding-top: 10px;
-}
+}

docs/build/html/_static/documentation_options.js

@@ -7,4 +7,4 @@ var DOCUMENTATION_OPTIONS = {
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',
     NAVIGATION_WITH_KEYS: false
-};
+};