Oldphysics docs

.docstr.yaml

@@ -0,0 +1,27 @@
+paths:
+  - tardis
+#badge: docs
+#exclude: .*/test # regex
+verbose: 2 # int (0-3)
+skip_magic: True
+skip_file_doc: True
+skip_init: True
+skip_class_def: False
+skip_private: True
+follow_links: True
+#ignore_names_file: .*/test # regex
+#fail_under: 90
+percentage_only: False
+#ignore_patterns: # Dict with key/value pairs of file-pattern/node-pattern
+#  .*: method_to_ignore_in_all_files
+#  FileWhereWeWantToIgnoreAllSpecialMethods: "__.+__"
+#  SomeFile:
+#    - method_to_ignore1
+#    - method_to_ignore2
+#    - method_to_ignore3
+#  a_very_important_view_file:
+#    - "^get$"
+#    - "^set$"
+#    - "^post$"
+#  detect_.*:
+#    - "get_val.*"

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,29 +1,35 @@
-<!--- Provide a general summary of your changes in the Title above -->
+<!--- Provide a general summary of your changes in the title above. -->
 
 ## Description
-<!--- Describe your changes in detail -->
+<!--- Describe your changes in detail. -->
 
 ## Motivation and Context
 <!--- Why is this change required? What problem does it solve? -->
 <!--- If it fixes an open issue, please link to the issue here. -->
 
 ## How Has This Been Tested?
+- [ ] Testing pipeline
+- [ ] Reference Data Comparison following these [instructions](https://tardis-sn.github.io/tardis/development/continuous_integration.html)
+- [ ] Other (please describe)
 <!--- Please describe in detail how you tested your changes. -->
 <!--- Include details of your testing environment, tests ran to see how -->
 <!--- your change affects other areas of the code, etc. -->
 
 ## Screenshots (if appropriate):
 
 ## Types of changes
-<!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
+<!--- Go over all the following points, and put an `x` in all the boxes that apply: -->
+<!--- What types of changes does your code introduce? -->
 - [ ] Bug fix (non-breaking change which fixes an issue)
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] None of the above (please describe)
 
 ## Checklist:
-<!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
+<!--- Go over all the following points, and put an `x` in all the boxes that apply: -->
 <!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
-- [ ] My code follows the code style of this project.
-- [ ] My change requires a change to the documentation.
-- [ ] I have updated the documentation accordingly.
-- [ ] I have assigned/requested two reviewers for this pull request.
+- [ ] My code follows the code style of this project
+- [ ] My change requires a change to the documentation
+- [ ] I have updated the documentation accordingly
+- [ ] I have built the documentation on my fork following [these instructions](https://tardis-sn.github.io/tardis/development/documentation_preview.html)
+- [ ] I have assigned and requested two reviewers for this pull request

.github/workflows/black-check.yml

@@ -0,0 +1,26 @@
+# For more information on how to use this template please refer to:
+# http://tardis-sn.github.io/tardis/development/continuous_integration.html
+
+name: black
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+
+      - name: Install Black
+        run: pip install black
+
+      - name: Run Black
+        run: black --check tardis

.github/workflows/docstr-coverage.yml

@@ -0,0 +1,37 @@
+name: docstr-coverage
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+
+      - name: Install docstr-coverage
+        run: pip install docstr-coverage
+
+      - name: Get base coverage
+        run: |
+          git checkout ${{ github.event.pull_request.base.sha }}
+          echo "BASE_COV=$(docstr-coverage -p)" >> $GITHUB_ENV
+
+      - name: Get head coverage
+        run: |
+          git checkout ${{ github.event.pull_request.head.sha }}
+          docstr-coverage --fail-under=$BASE_COV
+
+      - name: Blame
+        if: ${{ failure() }}
+        run: |
+          git diff --name-only $(git merge-base ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }}) | xargs docstr-coverage --accept-empty

.github/workflows/documentation-build.yml

@@ -1,13 +1,24 @@
+# For more information on how to use this template please refer to:
+# http://tardis-sn.github.io/tardis/development/continuous_integration.html
+
 name: documentation-build
 
 on:
   push:
     branches:
-      - master
+    - master
+
+  pull_request:
+    branches:
+    - master
+
+  schedule:
+    - cron: '10 0 * * 0'
 
 jobs:
   documentation_build:
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v2
 
@@ -16,7 +27,7 @@ jobs:
         with:
             environment-file: tardis_env3.yml
             activate-environment: tardis
-            channels: conda-forge, defaults
+            channels: conda-forge
             mamba-version: "*"
 
       - name: Install TARDIS

.github/workflows/update-changelog.yml

@@ -0,0 +1,34 @@
+# For more information on how to use this template please refer to:
+# http://tardis-sn.github.io/tardis/development/continuous_integration.html
+
+name: update-changelog
+
+on:
+  schedule:
+    - cron: '50 23 * * 0'
+
+jobs:
+  push:
+    runs-on: ubuntu-latest
+    if: ${{ github.repository_owner == 'tardis-sn' }}  # Do not run scheduled jobs on forks
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install github-changes
+        run: sudo npm install -g github-changes
+
+      - name: Update changelog
+        run: github-changes -o tardis-sn -r tardis --only-pulls --use-commit-body -f CHANGELOG.md -k ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "TARDIS Bot"
+          git add CHANGELOG.md
+          git commit -m "Update CHANGELOG.md [skip ci]"
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.BOT_TOKEN }}  # Use BOT_TOKEN to push on write-protected branches

.gitignore

@@ -5,6 +5,9 @@
 *.so
 __pycache__
 
+# Logging
+*.log
+
 
 # Ignore .c files by default to avoid including generated code. If you want to
 # add a non-generated .c extension, use `git add -f filename.c`.

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing to TARDIS
+# Contribution Guidelines
 
 So you are wondering how can you contribute to TARDIS? Congrats, you've landed on the right page!
 
@@ -38,7 +38,7 @@ Please make sure that you provide all the necessary information requested by pro
 
 There is always a scope of improvement in documentation to add some missing information or to make it easier for reading. And here lies an opportunity for you, since you can edit the documentation page you want which is stored as a text file in [`docs`](https://github.com/tardis-sn/tardis/tree/master/docs) directory of TARDIS.
 
-After editing the file locally, build the docs as described in [these instructions](#) and then you can submit your changes to us by making a patch as described in the next section.
+After editing the file locally, build the docs as described in [these instructions](https://tardis-sn.github.io/tardis/development/documentation_guidelines.html#building-documentation-locally) and then you can submit your changes to us by making a patch as described in the next section.
 
 ### Making a Patch
 
@@ -48,11 +48,10 @@ To contribute your code to TARDIS, you'll need to make a [pull request](https://
 
 When you make a pull request, please provide all the necessary information requested by prompts in the pull request body. Also, make sure that the code you're submitting always accounts for the following three:
 
-- **Maintaining code quality:** Your code must follow the PEP8 style guide, should cover edge cases, etc. Check our [code quality guidelines](#) for more details.
-- **Documenting the code:** You must write docstrings in functions/classes, put a relevant example in TARDIS docs and make sure docs get built correctly. To build the documentation locally, you can follow [this guide](#).
+- **Maintaining code quality:** Your code must follow the PEP8 style guide, should cover edge cases, etc. Check our [code quality guidelines](https://tardis-sn.github.io/tardis/development/code_quality.html) for more details.
+- **Documenting the code:** You must write docstrings in functions/classes, put a relevant example in TARDIS docs and make sure docs get built correctly. This is explained in detail in our [documentation guidelines](https://tardis-sn.github.io/tardis/development/documentation_guidelines.html).
 - **Testing the code:** There should be unit-tests for most of the functions/methods and they must pass our testing framework. To run test locally, you can follow [this guide](https://tardis-sn.github.io/tardis/development/running_tests.html).
 
-
 ### Spreading the word of mouth
 
 If you find TARDIS helpful, you can share it with your peers, colleagues, and anyone who can benefit from TARDIS. If you've used TARDIS in your research, please make sure to cite us (https://tardis-sn.github.io/tardis/credits.html). By telling other people about how we helped you, you'll help us in turn, in extending our impact. And we would absolutely love it if you give us a shout-out on [twitter](https://twitter.com/tardis_sn/)!

ah_bootstrap.py

@@ -918,7 +918,6 @@ def use_astropy_helpers(**kwargs):
 
     Parameters
     ----------
-
     path : str or None, optional
         A filesystem path relative to the root of the project's source code
         that should be added to `sys.path` so that `astropy_helpers` can be
@@ -933,32 +932,27 @@ def use_astropy_helpers(**kwargs):
         archive.
 
         If `None` skip straight to downloading.
-
     download_if_needed : bool, optional
         If the provided filesystem path is not found an attempt will be made to
         download astropy_helpers from PyPI.  It will then be made temporarily
         available on `sys.path` as a ``.egg`` archive (using the
         ``setup_requires`` feature of setuptools.  If the ``--offline`` option
         is given at the command line the value of this argument is overridden
         to `False`.
-
     index_url : str, optional
         If provided, use a different URL for the Python package index than the
         main PyPI server.
-
     use_git : bool, optional
         If `False` no git commands will be used--this effectively disables
         support for git submodules. If the ``--no-git`` option is given at the
         command line the value of this argument is overridden to `False`.
-
     auto_upgrade : bool, optional
         By default, when installing a package from a non-development source
         distribution ah_boostrap will try to automatically check for patch
         releases to astropy-helpers on PyPI and use the patched version over
         any bundled versions.  Setting this to `False` will disable that
         functionality. If the ``--offline`` option is given at the command line
         the value of this argument is overridden to `False`.
-
     offline : bool, optional
         If `False` disable all actions that require an internet connection,
         including downloading packages from the package index and fetching

azure-pipelines/compare-refdata.yml

@@ -13,22 +13,31 @@ schedules:
 
 variables:
   system.debug: false
+  results.url: 'http://opensupernova.org/~azuredevops/files/refdata-results'
+  commit.sha: '$(Build.SourceVersion)'
+  pr.number: '$(System.PullRequest.PullRequestNumber)'
+  #ref1.hash: ''
+  #ref2.hash: ''
 
-jobs:
-  - job: report
-    pool:
-      vmImage: 'ubuntu-latest'
+pool:
+  vmImage: 'ubuntu-latest'
 
+jobs:
+  - job: 'report'
     steps:
       - template: templates/default.yml
         parameters:
-          fetchRefdata: true
+          fetchRefdata: false  # See the comment below.
           useMamba: true
-
+
+      # Azure Repos requires token auth for public repositories containing LFS objects (bug).
+      # Fetch reference data from Azure with a PAT until a fix arrives.
       - bash: |
-          source activate tardis
-          $(package.manager) install bokeh --channel conda-forge --no-update-deps --yes
-        displayName: 'Install Bokeh'
+          MY_PAT=$(azure_pat)
+          B64_PAT=$(printf ":$MY_PAT" | base64)
+          git -c http.extraHeader="Authorization: Basic ${B64_PAT}" clone https://[email protected]/tardis-sn/TARDIS/_git/tardis-refdata $(refdata.dir)
+          cd $(refdata.dir); git -c http.extraHeader="Authorization: Basic ${B64_PAT}" lfs fetch --all
+        displayName: 'Fetch reference data repository'
 
       - bash: |
           cd $(refdata.dir)
@@ -42,6 +51,12 @@ jobs:
           source activate tardis
           pytest tardis --tardis-refdata=$(refdata.dir) --generate-reference
         displayName: 'Generate reference data'
+        condition: or(eq(variables['ref1.hash'], ''), eq(variables['ref2.hash'], ''))
+
+      - bash: |
+          source activate tardis
+          $(package.manager) install bokeh=2.2 --channel conda-forge --no-update-deps --yes
+        displayName: 'Install Bokeh'
 
       - bash: |
           cd $(refdata.dir)/notebooks
@@ -62,3 +77,34 @@ jobs:
           artifactName: 'report'
         displayName: 'Upload artifact'
         condition: succeededOrFailed()
+
+      - task: InstallSSHKey@0
+        inputs:
+         knownHostsEntry: $(opensupernova_host)
+         sshPublicKey: $(opensupernova_pubkey)
+         sshKeySecureFile: openSupernovaKey
+
+      - bash: |
+          ssh [email protected] "mkdir -p /home/azuredevops/public_html/files/refdata-results/$(pr.number)"
+          scp $(refdata.dir)/notebooks/ref_data_compare.html [email protected]:/home/azuredevops/public_html/files/refdata-results/$(pr.number)/$(commit.sha).html
+        displayName: 'Copy files to server'
+        condition: succeededOrFailed()
+
+      # Run only if the pipeline is triggered by a pull request.
+      - ${{ if eq(variables['Build.Reason'], 'PullRequest') }}:
+        - task: GitHubComment@0
+          inputs:
+            gitHubConnection: 'tardis-sn'
+            repositoryName: 'tardis-sn/tardis'
+            id: $(pr.number)
+            comment: '**Build succeeded** $(commit.sha) <br><br> [Click here]($(results.url)/$(pr.number)/$(commit.sha).html) to see results.'
+          displayName: 'Post results (success)'
+
+        - task: GitHubComment@0
+          inputs:
+            gitHubConnection: 'tardis-sn'
+            repositoryName: 'tardis-sn/tardis'
+            id: $(pr.number)
+            comment: '**Build failed** $(commit.sha) <br><br> [Click here]($(results.url)/$(pr.number)/$(commit.sha).html) to see results.'
+          displayName: 'Post results (failed)'
+          condition: failed()

docs/_templates/redirect_file.html

@@ -0,0 +1,14 @@
+<!DOCTYPE html>
+<html lang="en-US">
+  <head>
+    <meta charset="UTF-8" />
+    <meta http-equiv="refresh" content="1; url=#" />
+    <script type="text/javascript">
+      window.location.href = "#";
+    </script>
+    <title>Page Redirection</title>
+  </head>
+  <body>
+    If you are not redirected automatically, follow <a href="#">this link</a>.
+  </body>
+</html>