Merge branch 'master' into feature/add-support-for-combined-bosonic-a…

…nd-fermionic-heom-baths
hodgestar · Feb 13, 2023 · 44b19f5 · 44b19f5
2 parents 8059a4d + f3189a9
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -6,17 +6,12 @@ Thank you for contributing to QuTiP! Please make sure you have finished the foll
 You can use [pycodestyle](http://pycodestyle.pycqa.org/en/latest/index.html) to check your code automatically
 - [ ] Please add tests to cover your changes if applicable.
 - [ ] If the behavior of the code has changed or new feature has been added, please also update the documentation in the `doc` folder, and the [notebook](https://github.com/qutip/qutip-notebooks). Feel free to ask if you are not sure.
+- [ ] Include the changelog in a file named: `doc/changes/<PR number>.<type>` 'type' can be one of the following: feature, bugfix, doc, removal, misc, or deprecation (see [here](http://qutip.org/docs/latest/development/contributing.html#Changelog%20Generation) for more information).
 
 Delete this checklist after you have completed all the tasks. If you have not finished them all, you can also open a [Draft Pull Request](https://github.blog/2019-02-14-introducing-draft-pull-requests/) to let the others know this on-going work and keep this checklist in the PR description.
 
 **Description**
 Describe here the proposed change.
 
 **Related issues or PRs**
-Please mention the related issues or PRs here. If the PR fixes an issue, use the keyword fix/fixes/fixed followed by the issue id, e.g. fix #1184
-
-**Changelog**
-Give a short description of the PR in a few words. This will be shown in the QuTiP change log after the PR gets merged.
-For example: 
-Fixed error checking for null matrix in essolve.
-Added option for specifying resolution in Bloch.save function.
+Please mention the related issues or PRs here. If the PR fixes an issue, use the keyword fix/fixes/fixed followed by the issue id, e.g. fix #1184
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -12,14 +12,15 @@ on:
 
 
 jobs:
-  # The deploy_test job is part of the test of whether we should deploy to PyPI.
-  # The job will succeed if either the confirmation reference is empty or if the
-  # confirmation is the selected branch or tag name.  It will fail if it is
-  # nonempty and does not match.  All later jobs depend on this job, so that
-  # they will be immediately cancelled if the confirmation is bad.  The
-  # dependency is currently necessary (2021-03) because GitHub Actions does not
-  # have a simpler method of cancelling an entire workflow---the normal use-case
-  # expects to try and run as much as possible despite one or two failures.
+  # The deploy_test job is part of the test of whether we should deploy to PyPI
+  # or test.PyPI. The job will succeed if either the confirmation reference is
+  # empty, 'test' or if the confirmation is the selected branch or tag name.
+  # It will fail if it is nonempty and does not match.  All later jobs depend
+  # on this job, so that they will be immediately cancelled if the confirmation
+  # is bad.  The dependency is currently necessary (2021-03) because GitHub
+  # Actions does not have a simpler method of cancelling an entire workflow---
+  # the normal use-case expects to try and run as much as possible despite one
+  # or two failures.
   deploy_test:
     name: Verify PyPI deployment confirmation
     runs-on: ubuntu-latest
@@ -30,8 +31,10 @@ jobs:
       - name: Compare confirmation to current reference
         shell: bash
         run: |
-          [[ -z $CONFIRM_REF || $GITHUB_REF =~ ^refs/(heads|tags)/$CONFIRM_REF$ ]]
-          if [[ -z $CONFIRM_REF ]]; then
+          [[ -z $CONFIRM_REF || $GITHUB_REF =~ ^refs/(heads|tags)/$CONFIRM_REF$ || $CONFIRM_REF == "test" ]]
+          if [[ $CONFIRM_REF == "test" ]]; then
+            echo "Build and deploy to test.pypi.org."
+          elif [[ -z $CONFIRM_REF ]]; then
             echo "Build only.  Nothing will be uploaded to PyPI."
           else
             echo "Full build and deploy.  Wheels and source will be uploaded to PyPI."
@@ -46,15 +49,15 @@ jobs:
       OVERRIDE_VERSION: ${{ github.event.inputs.override_version }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           # For the sdist we should be as conservative as possible with our
           # Python version.  This should be the lowest supported version.  This
           # means that no unsupported syntax can sneak through.
-          python-version: '3.6'
+          python-version: '3.8'
 
       - name: Install pip build
         run: |
@@ -87,7 +90,7 @@ jobs:
           zip "$zipfile" -r "$stem"
           rm -r "$stem"
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: sdist
           path: |
@@ -104,27 +107,27 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
     env:
-      # Set up wheels matrix.  This is CPython 3.6--3.10 for all OS targets.
-      CIBW_BUILD: "cp3{6,7,8,9,10}-*"
-      # Numpy and SciPy do not supply wheels for i686 for Python 3.10, so we
-      # skip those too:
-      CIBW_SKIP: "*-musllinux* cp310-manylinux_i686 cp310-win32"
+      # Set up wheels matrix.  This is CPython 3.8--3.10 for all OS targets.
+      CIBW_BUILD: "cp3{8,9,10,11}-*"
+      # Numpy and SciPy do not supply wheels for i686 or win32 for
+      # Python 3.10+, so we skip those:
+      CIBW_SKIP: "*-musllinux* cp3{8,9,10,11}-manylinux_i686 cp3{8,9,10,11}-win32"
       OVERRIDE_VERSION: ${{ github.event.inputs.override_version }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           # This is about the build environment, not the released wheel version.
-          python-version: '3.7'
+          python-version: '3.8'
 
       - name: Install cibuildwheel
         run: |
           # cibuildwheel does the heavy lifting for us. Originally tested on
-          # 2.3.0, but should be fine at least up to any minor new release.
-          python -m pip install 'cibuildwheel==2.3.*'
+          # 2.11.3, but should be fine at least up to any minor new release.
+          python -m pip install 'cibuildwheel==2.11.*'
 
       - name: Build wheels
         shell: bash
@@ -134,7 +137,7 @@ jobs:
           if [[ ! -z "$OVERRIDE_VERSION" ]]; then echo "$OVERRIDE_VERSION" > VERSION; fi
           python -m cibuildwheel --output-dir wheelhouse
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: wheels
           path: ./wheelhouse/*.whl
@@ -143,10 +146,10 @@ jobs:
   deploy:
     name: "Deploy to PyPI if desired"
     # The confirmation is tested explicitly in `deploy_test`, so we know it is
-    # either a missing confirmation (so we shouldn't run this job) or a valid
-    # confirmation.  We don't need to retest the value of the confirmation,
-    # beyond checking that one existed.
-    if: ${{ github.event.inputs.confirm_ref != '' }}
+    # either a missing confirmation (so we shouldn't run this job), 'test' or a
+    # valid confirmation.  We don't need to retest the value of the
+    # confirmation, beyond checking that one existed.
+    if: ${{ github.event.inputs.confirm_ref != '' && github.event.inputs.confirm_ref != 'test' }}
     needs: [deploy_test, build_sdist, build_wheels]
     runs-on: ubuntu-latest
     env:
@@ -157,17 +160,17 @@ jobs:
 
     steps:
       - name: Download build artifacts to local runner
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.7'
+          python-version: '3.8'
 
       - name: Verify this is not a dev version
         shell: bash
         run: |
-          python -m pip install wheels/*-cp37-cp37m-*.manylinux2010_x86_64.whl
+          python -m pip install wheels/*-cp38-cp38-manylinux*.whl
           python -c 'import qutip; print(qutip.__version__); assert "dev" not in qutip.__version__; assert "+" not in qutip.__version__'
 
       # We built the zipfile for convenience distributing to Windows users on
@@ -176,3 +179,36 @@ jobs:
         run: |
           python -m pip install "twine"
           python -m twine upload --verbose wheels/*.whl sdist/*.tar.gz
+
+
+  deploy_testpypi:
+    name: "Deploy to TestPyPI if desired"
+    if: ${{ github.event.inputs.confirm_ref == 'test' }}
+    needs: [deploy_test, build_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    env:
+      TWINE_USERNAME: __token__
+      TWINE_PASSWORD: ${{ secrets.TESTPYPI_TOKEN }}
+      TWINE_NON_INTERACTIVE: 1
+
+    steps:
+      - name: Download build artifacts to local runner
+        uses: actions/download-artifact@v3
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Verify this is not a dev version
+        shell: bash
+        run: |
+          python -m pip install wheels/*-cp38-cp38-manylinux*.whl
+          python -c 'import qutip; print(qutip.__version__); assert "dev" not in qutip.__version__; assert "+" not in qutip.__version__'
+
+      # We built the zipfile for convenience distributing to Windows users on
+      # our end, but PyPI only needs the tarball.
+      - name: Upload sdist and wheels to TestPyPI
+        run: |
+          python -m pip install "twine"
+          python -m twine upload --repository testpypi --verbose wheels/*.whl sdist/*.tar.gz
diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml
@@ -1,4 +1,4 @@
-name: Build HTML documentation
+name: Build documentation
 
 on:
   [push, pull_request]
@@ -9,9 +9,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.8'
@@ -20,6 +20,8 @@ jobs:
         run: |
           pip install pip --upgrade
           python -mpip install -r doc/requirements.txt
+          sudo apt-get update
+          sudo apt-get install texlive-full
 
       - name: Install QuTiP from GitHub
         run: |
@@ -31,7 +33,23 @@ jobs:
           # because we're importing from the wrong location.
           python -c 'import qutip; qutip.about()'
 
-      - name: Build documentation
+      - name: Build PDF documentation
+        working-directory: doc
+        run: |
+          make latexpdf SPHINXOPTS="-W --keep-going -T"
+          # Above flags are:
+          #   -W : turn warnings into errors
+          #   --keep-going : do not stop after the first error
+          #   -T : display a full traceback if a Python exception occurs
+
+      - name: Upload built PDF files
+        uses: actions/upload-artifact@v3
+        with:
+          name: qutip_pdf_docs
+          path: doc/_build/latex/*
+          if-no-files-found: error
+
+      - name: Build HTML documentation
         working-directory: doc
         run: |
           make html SPHINXOPTS="-W --keep-going -T"
@@ -40,8 +58,8 @@ jobs:
           #   --keep-going : do not stop after the first error
           #   -T : display a full traceback if a Python exception occurs
 
-      - name: Upload built files
-        uses: actions/upload-artifact@v2
+      - name: Upload built HTML files
+        uses: actions/upload-artifact@v3
         with:
           name: qutip_html_docs
           path: doc/_build/html/*