Documentation formatting

.github/workflows/documentation-build.yml

@@ -19,6 +19,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
 
       - name: Setup TARDIS Environment 
         uses: conda-incubator/setup-miniconda@v2

.github/workflows/documentation-preview.yml

@@ -0,0 +1,55 @@
+# For more information on how to use this pipeline please refer to:
+# - http://tardis-sn.github.io/tardis/development/continuous_integration.html
+# - https://tardis-sn.github.io/tardis/development/documentation_preview.html
+
+name: documentation-preview
+
+on:
+  push:
+
+jobs:
+  documentation_preview:
+
+    # This workflow will be triggered:
+    #
+    # 1. Only on forks, never on main repository.
+    # 2. If the branch name contains the word `doc`.
+    # 3. If the commit message includes the tag `[build docs]`.
+
+    if: github.repository_owner != 'tardis-sn' && (contains(github.ref, 'doc') || contains(github.event.head_commit.message, '[build docs]'))
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Setup environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+            environment-file: tardis_env3.yml
+            activate-environment: tardis
+            use-mamba: true
+
+      - name: Install package
+        shell: bash -l {0}
+        run: python setup.py install
+
+      - name: Build documentation
+        shell: bash -l {0}
+        run: python setup.py build_docs
+
+      - name: Extract branch name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        id: extract_branch
+
+      - name: Deploy site
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: gh-pages
+          publish_dir: docs/_build/html/
+          destination_dir: branch/${{ steps.extract_branch.outputs.branch }}

CODE_OF_CONDUCT.md

@@ -15,4 +15,4 @@ As members of the community,
 
 This code of conduct has been adapted from the Astropy Code of Conduct, which in turn uses parts of the PSF code of conduct.
 
-**To report any violations of the code of conduct, please contact a member of the [TARDIS core team](https://tardis-sn.github.io/tardis/team.html) (the email tardis.supernova.code@gmail.com is monitored by the core team) or the Ombudsperson (see the [team page](https://tardis-sn.github.io/tardis/team.html); who is outside of the TARDIS collaboration and will treat reports confidentially).**
+**To report any violations of the code of conduct, please contact a member of the [TARDIS core team](https://tardis-sn.github.io/tardis/team_and_governance/team.html) (the email tardis.supernova.code@gmail.com is monitored by the core team) or the Ombudsperson (see the [team page](https://tardis-sn.github.io/tardis/team_and_governance/team.html); who is outside of the TARDIS collaboration and will treat reports confidentially).**

azure-pipelines/compare-refdata.yml

@@ -1,8 +1,19 @@
 # For more information on how to use this pipeline please refer to:
 # http://tardis-sn.github.io/tardis/development/continuous_integration.html
 
+# IMPORTANT: Only contributors with `Write` permission can trigger the build
+#            by commenting `/AzurePipelines run <pipeline-name>` on the pull
+#            request.
+#
+#            This feature can be disabled only through the Azure Pipelines
+#            dashboard.
+
 trigger: none
-pr: [ master ]
+
+pr:
+  branches:
+    include:
+    - '*'
 
 schedules:
   - cron: '0 0 1 * *'
@@ -30,6 +41,11 @@ jobs:
           fetchRefdata: false  # See the comment below.
           useMamba: true
 
+      - bash: |
+          source activate tardis
+          $(package.manager) install bokeh=2.2 --channel conda-forge --no-update-deps --yes
+        displayName: 'Install Bokeh'
+
       # 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: |
@@ -53,11 +69,6 @@ jobs:
         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
           source activate tardis

azure-pipelines/run-unit-tests.yml

@@ -2,7 +2,14 @@
 # http://tardis-sn.github.io/tardis/development/continuous_integration.html
 
 trigger:
-  - master
+  branches:
+    include:
+    - '*'
+
+pr:
+  branches:
+    include:
+    - '*'
 
 variables:
   codecov.token: 'a876d307-9ed5-4f5d-a6c4-e58291ac4111'

azure-pipelines/update-refdata.yml

@@ -0,0 +1,74 @@
+# For more information on how to use this pipeline please refer to:
+# http://tardis-sn.github.io/tardis/development/continuous_integration.html
+
+# IMPORTANT: Only contributors with `Write` permission can trigger the build
+#            by commenting `/AzurePipelines run <pipeline-name>` on the pull
+#            request.
+#
+#            This feature can be disabled only through the Azure Pipelines
+#            dashboard.
+
+trigger: none
+
+pr:
+  branches:
+    include:
+    - master
+
+variables:
+  system.debug: false
+  commit.sha: '$(Build.SourceVersion)'
+  pr.number: '$(System.PullRequest.PullRequestNumber)'
+  build.id: '$(Build.BuildId)'
+  job.id: '$(System.JobId)'
+  log.url: 'https://dev.azure.com/tardis-sn/TARDIS/_build/results?buildId=$(build.id)&view=logs&jobId=$(job.id)'
+
+pool:
+  vmImage: 'ubuntu-latest'
+
+jobs:
+  - job: 'push'
+    steps:
+      - template: templates/default.yml
+        parameters:
+          fetchRefdata: false  # We don't want to fetch from the mirror
+          useMamba: true
+          skipInstall: false
+
+      - bash: git clone https://github.com/tardis-sn/tardis-refdata $(refdata.dir)
+        displayName: 'Fetch reference data repository'
+
+      - bash: |
+          cd $(tardis.dir)
+          source activate tardis
+          pytest tardis --tardis-refdata=$(refdata.dir) --generate-reference
+        displayName: 'Generate reference data'
+
+      - bash: |
+          cd $(refdata.dir)
+          git add unit_test_data.h5
+          git config --local user.email "wkerzendorf+tardis@gmail.com"
+          git config --local user.name "TARDIS Bot"
+          git commit -m "update reference data (pr $(pr.number))"
+          git remote set-url origin https://$(bot_token)@github.com/tardis-sn/tardis-refdata
+          git push origin master
+        displayName: 'Push new reference data'
+
+      # 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: '**Update succeeded** $(commit.sha) <br><br> Changes pushed to [tardis-sn/tardis-refdata](/tardis-sn/tardis-refdata).'
+          displayName: 'Post results (success)'
+
+        - task: GitHubComment@0
+          inputs:
+            gitHubConnection: 'tardis-sn'
+            repositoryName: 'tardis-sn/tardis'
+            id: $(pr.number)
+            comment: '**Update failed** $(commit.sha) <br><br> For more information, check the [job log]($(log.url)).'
+          displayName: 'Post results (failed)'
+          condition: failed()

docs/conf.py

@@ -100,7 +100,7 @@
 # This does not *have* to match the package name, but typically does
 project = "TARDIS"
 author = "TARDIS collaboration"
-copyright = "{0}-{1}, {2}".format(2013, datetime.datetime.now().year, author)
+copyright = f"{2013}-{datetime.datetime.now().year}, {author}"
 
 master_doc = "index"
 # default_role = 'obj'
@@ -157,7 +157,8 @@
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = "{0} v{1}".format(project, release)
+
+html_title = f"{project} v{release}"
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = project + "doc"
@@ -199,6 +200,13 @@ def to_html_ext(path):
     return os.path.splitext(path)[0] + ".html"
 
 
+def autodoc_skip_member(app, what, name, obj, skip, options):
+    """Exclude specific functions/methods from the documentation"""
+    exclusions = ("yaml_constructors", "yaml_implicit_resolvers")
+    exclude = name in exclusions
+    return skip or exclude
+
+
 def create_redirect_files(app, docname):
     """Create redirect html files at old paths specified in `redirects` list."""
     template_html_path = os.path.join(
@@ -223,4 +231,5 @@ def create_redirect_files(app, docname):
 
 
 def setup(app):
+    app.connect("autodoc-skip-member", autodoc_skip_member)
     app.connect("build-finished", create_redirect_files)