Merge pull request #1 from tardis-sn/master

Updating my Version of Tardis and Fixing Environment

.github/FUNDING.yml

@@ -0,0 +1,15 @@
+# These are supported funding model platforms
+
+# github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
+# patreon: # Replace with a single Patreon username
+# open_collective: # Replace with a single Open Collective username
+# ko_fi: # Replace with a single Ko-fi username
+# tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+# community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+# liberapay: # Replace with a single Liberapay username
+# issuehunt: # Replace with a single IssueHunt username
+# otechie: # Replace with a single Otechie username
+# custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']
+
+github: numfocus
+custom: https://numfocus.org/donate-to-tardis

.github/workflows/documentation-build.yml

@@ -0,0 +1,35 @@
+name: documentation-build
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  documentation_build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup TARDIS Environment 
+        uses: conda-incubator/setup-miniconda@v1 
+        with:
+            environment-file: tardis_env3.yml
+            activate-environment: tardis
+            channels: conda-forge, defaults
+            mamba-version: "*"
+
+      - name: Install TARDIS
+        shell: bash -l {0}
+        run: python setup.py install 
+
+      - name: Build Sphinx Documentation
+        shell: bash -l {0}
+        run: python setup.py build_docs
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html/
+          publish_branch: gh-pages

.gitignore

@@ -18,6 +18,7 @@ __pycache__
 htmlcov
 .coverage
 .ipynb_checkpoints/
+.pytest_cache/
 
 
 # IDE Specific files
@@ -71,6 +72,3 @@ distribute-*.tar.gz
 
 # Mac OSX
 .DS_Store
-
-# Jupyter checkpoints
-.ipynb_checkpoints

README.rst

@@ -20,6 +20,13 @@ TARDIS
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/psf/black
 
+.. image:: https://img.shields.io/badge/Donate-to%20TARDIS-brightgreen.svg
+    :target: https://numfocus.salsalabs.org/donate-to-tardis/index.html
+
+.. image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
+    :target: http://numfocus.org
+    :alt: Powered by NumFOCUS
+
 TARDIS is a tool that creates synthetic observations (spectra) for exploding
 stars (supernovae).
 

azure-pipelines/compare-refdata.yml

@@ -1,73 +1,64 @@
-# Starter pipeline
-# Start with a minimal pipeline that you can customize to build and deploy your code.
-# Add steps that build, run tests, deploy, and more:
-# https://aka.ms/yaml
+# For more information on how to use this pipeline please refer to:
+# http://tardis-sn.github.io/tardis/development/continuous_integration.html
 
 trigger: none
-pr: none
+pr: [ master ]
+
+schedules:
+  - cron: '0 0 1 * *'
+    displayName: 'Monthly test'
+    branches:
+      include:
+        - master
 
 variables:
-  system.debug: "true"
-  ref.data.home: "$(Agent.BuildDirectory)/tardis-refdata"
-  ref.data.github.url: "https://github.com/tardis-sn/tardis-refdata.git"
-  tardis.build.dir: $(Build.Repository.LocalPath)
+  system.debug: false
 
 jobs:
   - job: report
     pool:
-      vmImage: "ubuntu-latest"
+      vmImage: 'ubuntu-latest'
 
     steps:
-      - bash: |
-          echo "##vso[task.prependpath]$CONDA/bin"
-          sudo chown -R $USER $CONDA
-        displayName: "Add CONDA to path"
-
-      - bash: |
-          sh ci-helpers/install_tardis_env.sh
-        displayName: "Install TARDIS env"
-
+      - template: templates/default.yml
+        parameters:
+          fetchRefdata: true
+          useMamba: true
+
       - bash: |
           source activate tardis
-          conda install bokeh -c conda-forge --no-update-deps --yes
-        displayName: "Install Bokeh"
+          $(package.manager) install bokeh --channel conda-forge --no-update-deps --yes
+        displayName: 'Install Bokeh'
 
       - bash: |
-          source activate tardis
-          git clone https://github.com/tardis-sn/tardis-refdata.git $(ref.data.home)
-        displayName: "Fetch ALL reference data"
+          cd $(refdata.dir)
+          git remote add upstream https://tardis-sn@dev.azure.com/tardis-sn/TARDIS/_git/tardis-refdata
+          git fetch upstream
+          git fetch upstream "+refs/pull/*/head:refs/remotes/upstream/pr/*"
+        displayName: 'Set upstream remote'
 
       - bash: |
+          cd $(tardis.dir)
           source activate tardis
-          python setup.py build_ext --inplace
-        displayName: "Build & install TARDIS"
+          pytest tardis --tardis-refdata=$(refdata.dir) --generate-reference
+        displayName: 'Generate reference data'
 
       - bash: |
+          cd $(refdata.dir)/notebooks
           source activate tardis
-          python setup.py test --args="--tardis-refdata=$(ref.data.home) --generate-reference"
-        displayName: "Generate new reference data"
+          jupyter nbconvert ref_data_compare.ipynb --to html --execute --ExecutePreprocessor.timeout=6000
+        displayName: 'Render notebook'
 
       - bash: |
+          cd $(refdata.dir)/notebooks
           source activate tardis
-          cd $(ref.data.home)
-          git remote add upstream https://github.com/tardis-sn/tardis-refdata.git
-          git fetch upstream
-          git fetch upstream "+refs/pull/*/head:refs/remotes/upstream/pr/*"
-          cd notebooks
           jupyter nbconvert ref_data_compare.ipynb --to html --execute --allow-errors --ExecutePreprocessor.timeout=6000
-        displayName: "Generating report"
+        displayName: 'Render notebook (allow errors)'
+        condition: failed()
 
       - task: PublishPipelineArtifact@1
         inputs:
-          targetPath: "$(ref.data.home)/notebooks/ref_data_compare.html"
-          artifact: "report"
-          publishLocation: "pipeline"
-
-      - bash: |
-          ls -lR /tmp
-          echo
+          targetPath: '$(refdata.dir)/notebooks/ref_data_compare.html'
+          artifactName: 'report'
+        displayName: 'Upload artifact'
         condition: succeededOrFailed()
-        displayName: "Check files in /tmp"
-
-# Keep this line, is useful for testing without changing the notebook.
-# sed -i "s/ref2_hash='upstream\/pr\/24'/ref1_hash='c998f44', ref2_hash='master'/g" ref_data_compare.ipynb

azure-pipelines/release-version.yml

@@ -1,61 +1,47 @@
-# Starter pipeline
-# Start with a minimal pipeline that you can customize to build and deploy your code.
-# Add steps that build, run tests, deploy, and more:
-# https://aka.ms/yaml
+# For more information on how to use this pipeline please refer to:
+# http://tardis-sn.github.io/tardis/development/continuous_integration.html
 
 trigger: none
 pr: none
+
 schedules:
-  - cron: "30 22 * * 0"
-    displayName: Weekly build
+  - cron: '0 0 * * 0'
+    displayName: 'Weekly release'
     branches:
       include:
         - master
-    always: true
+    always: false
 
 variables:
-  system.debug: "true"
-  tardis.build.dir: $(Build.Repository.LocalPath)
+  system.debug: false
 
 pool:
-  vmImage: "ubuntu-latest"
+  vmImage: 'ubuntu-latest'
 
 jobs:
-  - job: gh_release
-    displayName: Upload GitHub release
-    steps:
-      - bash: |
-          echo "##vso[task.prependpath]$CONDA/bin"
-          sudo chown -R $USER $CONDA
-        displayName: "Add CONDA to path"
-
-      - bash: |
-          sh ci-helpers/install_tardis_env.sh
-        displayName: "Install TARDIS env"
+  - job: release
+    displayName: 'TARDIS release'
 
-      - bash: |
-          source activate tardis
-          python setup.py install
-        displayName: "Build & install TARDIS"
+    steps:
+      - template: templates/default.yml
+        parameters:
+          useMamba: true
 
       - bash: |
+          cd $(tardis.dir)
           source activate tardis
           echo "##vso[task.setvariable variable=version]$(python -c 'import tardis; print(tardis.__version__)')"
-        displayName: "Get TARDIS version number"
-
-      - bash: |
-          echo $(VERSION)
-        displayName: "Recover TARDIS version number"
+        displayName: 'Get TARDIS version'
 
       - task: GitHubRelease@1
         inputs:
-          gitHubConnection: "wkerzendorf"
-          repositoryName: "$(Build.Repository.Name)"
-          action: "create"
-          target: "$(Build.SourceVersion)"
-          tagSource: "userSpecifiedTag"
-          tag: "v$(VERSION)"
-          title: "TARDIS v$(VERSION)"
-          isPreRelease: false
-          changeLogCompareToRelease: "lastFullRelease"
-          changeLogType: "commitBased"
+          gitHubConnection: 'wkerzendorf'
+          repositoryName: '$(Build.Repository.Name)'
+          action: 'create'
+          target: '$(Build.SourceVersion)'
+          tagSource: 'userSpecifiedTag'
+          tag: 'v$(version)'
+          title: 'TARDIS v$(version)'
+          changeLogCompareToRelease: 'lastFullRelease'
+          changeLogType: 'commitBased'
+        displayName: 'Create GitHub Release'

azure-pipelines/simple_test_framework.yml → azure-pipelines/run-unit-tests.yml

@@ -9,18 +9,16 @@ variables:
   system.debug: false
 
 jobs:
-  - job: test
-    displayName: 'TARDIS test'
-
+  - job:
     pool:
       vmImage: $[variables.vm_Image]
 
     strategy:
       matrix:
-        linux:
+        Linux:
           vm_Image: 'ubuntu-latest'
 
-        mac:
+        macOS:
           vm_Image: 'macOS-latest'
 
       maxParallel: 2