Update copier template version

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: v0.11.0
+_commit: v0.14.2
 _src_path: gl:znicholls/copier-core-python-repository
 conda_release: false
 email: zebedee.nicholls@climate-energy-college.org

.github/actions/setup/action.yml

@@ -20,7 +20,7 @@ runs:
       id: setup-uv
       uses: astral-sh/setup-uv@v4
       with:
-        version: "0.5.21"
+        version: "0.8.8"
         python-version: ${{ inputs.python-version }}
     - name: Install dependencies
       shell: bash

.github/workflows/bump.yaml

@@ -1,25 +1,21 @@
 name: Bump version
-# For the time being, we still do this with pdm.
-# Honestly, it doesn't really matter,
-# but one day uv will have a bump command too and we can switch to that.
-# Relevant issue in uv: https://github.com/astral-sh/uv/issues/6298
 
 on:
   workflow_dispatch:
     inputs:
       bump_rule:
         type: choice
-        description: How to bump the project's version (see https://github.com/carstencodes/pdm-bump#usage)
+        description: How to bump the project's version (see https://docs.astral.sh/uv/reference/cli/#uv-version)
         options:
-          - no-pre-release
-          # no micro because we always sit on a pre-release in main,
-          # so we would always use no-pre-release instead of micro
-          # - micro
+          - patch
           - minor
           - major
-          - "pre-release --pre alpha"
-          - "pre-release --pre beta"
-          - "pre-release --pre release-candidate"
+          - stable
+          - alpha
+          - beta
+          - rc
+          - post
+          - dev
         required: true
 
 jobs:
@@ -29,7 +25,7 @@ jobs:
     strategy:
       matrix:
         os: [ "ubuntu-latest" ]
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
     runs-on: "${{ matrix.os }}"
     env:
       CI_COMMIT_EMAIL: "ci-runner@openscm-zenodo.invalid"
@@ -40,15 +36,6 @@ jobs:
           fetch-depth: 0
           token: "${{ secrets.PERSONAL_ACCESS_TOKEN }}"
 
-      - name: Setup PDM
-        uses: pdm-project/setup-pdm@v4.1
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install pdm-bump
-        run: |
-          pdm self add pdm-bump
-
       - uses: ./.github/actions/setup
         with:
           python-version: ${{ matrix.python-version }}
@@ -59,13 +46,13 @@ jobs:
           git config --global user.name "$GITHUB_ACTOR"
           git config --global user.email "$CI_COMMIT_EMAIL"
 
-          BASE_VERSION=`sed -ne 's/^version = "\([0-9\.a]*\)"/\1/p' pyproject.toml`
+          BASE_VERSION=`sed -ne 's/^version = "\([0-9\.post]*\)"/\1/p' pyproject.toml`
           echo "Bumping from version $BASE_VERSION"
 
           # Bump
-          pdm bump ${{ github.event.inputs.bump_rule }}
+          uv version --bump ${{ github.event.inputs.bump_rule }}
 
-          NEW_VERSION=`sed -ne 's/^version = "\([0-9\.a]*\)"/\1/p' pyproject.toml`
+          NEW_VERSION=`sed -ne 's/^version = "\([0-9\.]*\)"/\1/p' pyproject.toml`
           echo "Bumping to version $NEW_VERSION"
 
           # Build CHANGELOG
@@ -78,12 +65,12 @@ jobs:
 
           # Bump to alpha (so that future commits do not have the same
           # version as the tagged commit)
-          BASE_VERSION=`sed -ne 's/^version = "\([0-9\.a]*\)"/\1/p' pyproject.toml`
+          BASE_VERSION=`sed -ne 's/^version = "\([0-9\.]*\)"/\1/p' pyproject.toml`
 
           # Bump to pre-release of next version
-          pdm bump pre-release --pre alpha
+          uv version --bump post
 
-          NEW_VERSION=`sed -ne 's/^version = "\([0-9\.a]*\)"/\1/p' pyproject.toml`
+          NEW_VERSION=`sed -ne 's/^version = "\([0-9\.post]*\)"/\1/p' pyproject.toml`
           echo "Bumping version $BASE_VERSION > $NEW_VERSION"
 
           # Commit and push

.github/workflows/ci.yaml

@@ -143,7 +143,7 @@ jobs:
         id: setup-uv
         uses: astral-sh/setup-uv@v4
         with:
-          version: "0.5.21"
+          version: "0.8.8"
           python-version: ${{ matrix.python-version }}
       - name: Create venv
         run: |
@@ -187,8 +187,9 @@ jobs:
       - name: Install
         run: |
           pip install --upgrade pip wheel
-          pip install .
-          pip install -r requirements-only-tests-locked.txt
+          pip install --no-deps .
+          pip install -r requirements-locked.txt
+          pip install -r requirements-only-tests-min-locked.txt
       - name: Run tests
         run: |
           pytest tests -r a -vv tests
@@ -204,12 +205,17 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-      - uses: ./.github/actions/setup
+      - name: Set up Python "${{ matrix.python-version }}"
+        id: setup-python
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-          uv-dependency-install-flags: "--no-dev"  # no extras is default
+          python-version: "${{ matrix.python-version }}"
+      - name: Install
+        run: |
+          pip install --upgrade pip wheel
+          pip install .
       - name: Check importable without extras
-        run: uv run python scripts/test-install.py
+        run: python scripts/test-install.py
 
   check-build:
     strategy:
@@ -224,11 +230,15 @@ jobs:
         id: setup-uv
         uses: astral-sh/setup-uv@v4
         with:
-          version: "0.5.21"
+          version: "0.8.8"
           python-version: ${{ matrix.python-version }}
       - name: Build package
         run: |
+          uv run python scripts/add-locked-targets-to-pyproject-toml.py
+          cat pyproject.toml
           uv build
+          # Just in case, undo the changes to `pyproject.toml`
+          git restore --staged . && git restore .
       - name: Check build
         run: |
           tar -tvf dist/openscm_zenodo-*.tar.gz --wildcards '*openscm_zenodo/py.typed'

.github/workflows/deploy.yaml

@@ -32,9 +32,12 @@ jobs:
         id: setup-uv
         uses: astral-sh/setup-uv@v4
         with:
-          version: "0.5.21"
+          version: "0.8.8"
           python-version: ${{ matrix.python-version }}
       - name: Publish to PyPI
         run: |
+          uv run python scripts/add-locked-targets-to-pyproject-toml.py
           uv build
           uv publish
+          # Just in case, undo the changes to `pyproject.toml`
+          git restore --staged . && git restore .

.github/workflows/release.yaml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ "ubuntu-latest" ]
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
     runs-on: "${{ matrix.os }}"
     steps:
       - name: Check out repository
@@ -25,15 +25,18 @@ jobs:
         id: setup-uv
         uses: astral-sh/setup-uv@v4
         with:
-          version: "0.5.21"
+          version: "0.8.8"
           python-version: ${{ matrix.python-version }}
       - name: Add version to environment
         run: |
-          PROJECT_VERSION=`sed -ne 's/^version = "\([0-9\.a]*\)"/\1/p' pyproject.toml`
+          PROJECT_VERSION=`sed -ne 's/^version = "\([0-9\.]*\)"/\1/p' pyproject.toml`
           echo "PROJECT_VERSION=$PROJECT_VERSION" >> $GITHUB_ENV
       - name: Build package for PyPI
         run: |
+          uv run python scripts/add-locked-targets-to-pyproject-toml.py
           uv build
+          # Just in case, undo the changes to `pyproject.toml`
+          git restore --staged . && git restore .
       - name: Generate Release Notes
         run: |
           echo "" >> ".github/release_template.md"

.github/workflows/test-upstream-latest.yaml

@@ -36,7 +36,7 @@ jobs:
         id: setup-uv
         uses: astral-sh/setup-uv@v4
         with:
-          version: "0.5.21"
+          version: "0.8.8"
           python-version: ${{ matrix.python-version }}
       # Often you need a step like this for e.g. numpy, scipy, pandas
       - name: Setup compilation dependencies

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
   autoupdate_schedule: quarterly
   autoupdate_branch: pre-commit-autoupdate
   # Currently network access isn't supported in the pre-commit CI product.
-  skip: [uv-sync, uv-lock, uv-export, pdm-lock-check]
+  skip: [uv-sync, uv-lock, uv-export]
 
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
@@ -60,19 +60,3 @@ repos:
         args: ["-o", "requirements-only-tests-locked.txt", "--no-hashes", "--no-dev", "--no-emit-project", "--only-group", "tests"]
       # # Not released yet
       # - id: uv-sync
-  - repo: https://github.com/pdm-project/pdm
-    rev: 2.22.1
-    hooks:
-      # Update the `pdm.lock` file if needed.
-      # We need the pdm lock file too
-      # so that we can build the locked version of the package.
-      - name: pdm-lock
-        id: pdm-lock-check
-        # Overwrite the hook's standard entry point to get the behaviour we want
-        entry: pdm lock
-        args: ["--group", ":all", "--strategy", "inherit_metadata"]
-        files: ^pyproject.toml$
-        pass_filenames: false
-      # Double check that the `pdm.lock` file is up to date.
-      - id: pdm-lock-check
-        args: ["--group", ":all", "--strategy", "inherit_metadata"]

Makefile

@@ -38,7 +38,7 @@ ruff-fixes:  ## fix the code using ruff
 
 .PHONY: test
 test:  ## run the tests
-	uv run pytest src tests -r a -v --doctest-modules --cov=src
+	uv run pytest src tests -r a -v --doctest-modules --doctest-report ndiff --cov=src
 
 # Note on code coverage and testing:
 # You must specify cov=src.
@@ -80,12 +80,6 @@ licence-check:  ## Check that licences of the dependencies are suitable
 	uv run liccheck -r $(TEMP_FILE) -R licence-check.txt
 	rm -f $(TEMP_FILE)
 
-.PHONY: pdm-lock
-pdm-lock: pdm.lock  ## create/update the `pdm.lock` file
-
-pdm.lock: pyproject.toml
-	pdm lock --group :all --strategy inherit_metadata
-
 .PHONY: virtual-environment
 virtual-environment:  ## update virtual environment, create a new one if it doesn't already exist
 	uv sync --all-extras --group all-dev

changelog/18.trivial.md

@@ -0,0 +1 @@
+Updated to the latest version of the copier template

docs/development.md

@@ -48,16 +48,16 @@ should change depending on the updates to the code base.
 Releasing is semi-automated via a CI job.
 The CI job requires the type of version bump
 that will be performed to be manually specified.
-See the pdm-bump docs for the
-[list of available bump rules](https://github.com/carstencodes/pdm-bump#usage).
+See the `uv version` docs (specifically the `--bump` flag) for the
+[list of available bump rules](https://docs.astral.sh/uv/reference/cli/#uv-version).
 
 ### Standard process
 
 The steps required are the following:
 
 1. Bump the version: manually trigger the "bump" workflow from the main branch
    (see here: [bump workflow](https://github.com/openscm/OpenSCM-zenodo/actions/workflows/bump.yaml)).
-   A valid "bump_rule" (see [pdm-bump's docs](https://github.com/carstencodes/pdm-bump#usage))
+   A valid "bump_rule" (see [uv's docs](https://docs.astral.sh/uv/reference/cli/#uv-version))
    will need to be specified.
    This will then trigger a draft release.
 
@@ -74,16 +74,15 @@ The steps required are the following:
    else
 
 1. Enjoy the newly available version
+[TODO: add in conda release instructions]
 
 #### Further details
 
-We use [pdm](https://pdm-project.org/en/latest/) for building our project,
-while [uv figures out how it wants to support building](https://github.com/astral-sh/uv/issues/3957).
-This gives us the added benefit that we can use
-[pdm-build-locked](https://pdm-build-locked.readthedocs.io/en/stable/)
-to build locked versions of our package.
-It is for these reasons that we have a pdm pre-commit hook
-and a `pdm.lock` file in our repository.
+We use [uv's build backend](https://docs.astral.sh/uv/concepts/build-backend) for building our project
+and `scripts/add-locked-targets-to-pyproject-toml.py`
+to provide locked extra groups for our package.
+Including locked extra groups is why we run `scripts/add-locked-targets-to-pyproject-toml.py`
+before any step related to building the package in the CI.
 
 ## Read the Docs
 

docs/further-background/dependency-pinning-and-testing.md

@@ -24,8 +24,7 @@ In the majority of cases, new releases do not cause issues
 so pinning simply forces users to workaround overly strict pins[^1]
 (which can be done, see
 [working around incorrectly set pins][working-around-incorrectly-set-pins]).
-The tradeoff with this approach is
-This does run the risk that,
+The tradeoff with this approach is that you run the risk that,
 if a dependency releases a breaking change,
 the function provided by our package may break too.
 
@@ -128,12 +127,12 @@ Finally, we also check the installation of the locked versions of the package,
 i.e. installation with `pip install 'openscm-zenodo[locked]'`.
 These tests give us the greatest coverage of Python versions and operating systems
 and help alert us to places where users may face issues.
-Having said that, these tests do require 30 separate CI runs,
+Having said that, these tests do require 30 separate jobs,
 which is why we don't run them in CI.
 
 Through this combination of CI testing and installation testing,
 we get a pretty good coverage of the different ways in which our package can be used.
 It is not perfect, largely because the combinatorics don't allow for testing everything.
 If we find a particular, key, use case failing often,
 then we would happily discuss whether this should be included in the CI too,
-to catch issues earlier than at user time.
+to catch issues in advance of use.

mkdocs.yml

@@ -70,7 +70,7 @@ plugins:
       handlers:
         python_xref:
           paths: [src]
-          import:
+          inventories:
             # Cross-ref helpers (lots included here, remove what you don't want)
             - https://www.attrs.org/en/stable/objects.inv
             - https://unidata.github.io/cftime/objects.inv
@@ -87,11 +87,25 @@ plugins:
             - https://docs.scipy.org/doc/scipy/objects.inv
             - https://scitools-iris.readthedocs.io/en/stable/objects.inv
             - https://scmdata.readthedocs.io/en/stable/objects.inv
+            # # Not available for tqdm
+            # # https://github.com/tqdm/tqdm/issues/705
+            # - https://tqdm.github.io/objects.inv
             - https://validators.readthedocs.io/en/stable/objects.inv
             - http://xarray.pydata.org/en/stable/objects.inv
           options:
+            # It turns out that xref does this check without considering config.
+            # As a result, every docstring is parsed as a google-style docstring.
+            # As docstrings are only parsed once, this results in rendering failures.
+            # Hence, turn off the checks here.
+            # mkdocs_autorefs catches anything which doesn't end up being a correct reference.
+            # The fix might be as simple as changing
+            # `self.collect(ref, PythonOptions())`
+            # to `self.collect(ref, self.get_options({}))`
+            # in the python-xref source, but it's hard to predict the side effects
+            # so we haven't bothered with that route.
+            check_crossrefs: false
             docstring_style: numpy
-            relative_crossrefs: yes
+            relative_crossrefs: true
             separate_signature: true
             show_root_heading: false
             show_signature_annotations: true
@@ -111,6 +125,7 @@ plugins:
 markdown_extensions:
   # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#attribute-lists
   - attr_list
+  - footnotes
   # https://squidfunk.github.io/mkdocs-material/reference/math/#katex-mkdocsyml
   - pymdownx.arithmatex:
       generic: true