Update to using copier template

.copier-answers.yml

@@ -0,0 +1,15 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: v0.4.1
+_src_path: gl:znicholls/copier-core-python-repository
+email: [email protected]
+include_cli: true
+name: Zebedee Nicholls
+notebook_based_docs: true
+pandas_doctests: false
+plot_dependencies: false
+project_description_short: Command-line tool for uploading to zenodo.
+project_name_human: OpenSCM Zenodo
+project_name_pip: openscm-zenodo
+project_name_python: openscm_zenodo
+project_url: https://github.com/openscm/OpenSCM-zenodo
+track_lock_file: true

.github/ISSUE_TEMPLATE/bug.md

@@ -35,7 +35,6 @@ def test_bug_12():
 
  - OS: [e.g. Windows, Linux, macOS]
  - Python version [e.g. Python 3.11]
- - Please also upload your `poetry.lock` file (first run `poetry lock` to make sure the lock file is up-to-date)
 
 ## Additional context
 <!--- Add any other context about the problem here. -->

.github/workflows/ci.yaml

@@ -16,7 +16,7 @@ jobs:
       - uses: ./.github/actions/setup
         with:
           python-version: "3.11"
-          pdm-dependency-install-flags: "-G dev"
+          pdm-dependency-install-flags: "-G :all"
       - name: mypy
         run: |
           MYPYPATH=stubs pdm run mypy src
@@ -30,11 +30,17 @@ jobs:
       - uses: ./.github/actions/setup
         with:
           python-version: "3.11"
-          pdm-dependency-install-flags: "-G docs -G dev"
+          pdm-dependency-install-flags: "-G docs -G :all"
       - name: docs
         run: |
           pdm run typer openscm_zenodo.cli utils docs --output docs/cli/index.md --name openscm-zenodo
           pdm run mkdocs build --strict
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "3.11"
+          pdm-dependency-install-flags: "-G docs -G :all -G dev"
+      - name: docs-with-changelog
+        run: |
           # Check CHANGELOG will build too
           pdm run towncrier build --yes
           pdm run mkdocs build --strict
@@ -61,11 +67,16 @@ jobs:
       - uses: ./.github/actions/setup
         with:
           python-version: ${{ matrix.python-version }}
-          pdm-dependency-install-flags: "-G tests"
-          # TODO: sort out zenodo token
+          # When running the tests, install with all optional dependencies
+          # to get maximum test coverage.
+          # If we find that we're getting failures
+          # when people try to run without installing optional dependencies,
+          # we should add a CI step that runs the tests without optional dependencies too.
+          # We don't have that right now, because we're not sure this pain point exists.
+          pdm-dependency-install-flags: "-G :all -G tests"
       - name: Run tests
         run: |
-          pdm run pytest -r a -v src tests --doctest-modules
+          pdm run pytest -r a -v src tests
       - name: Run tests with zenodo token
         # Only run these on one machine to avoid CI fighting each other by modifying the same Zenodo record
         if: ${{ (matrix.python-version == '3.11') && (matrix.os == 'ubuntu-latest') }}
@@ -90,7 +101,7 @@ jobs:
       - uses: ./.github/actions/setup
         with:
           python-version: ${{ matrix.python-version }}
-          pdm-dependency-install-flags: "--prod"
+          pdm-dependency-install-flags: "--prod --without :all"
       - name: Check importable without extras
         run: pdm run python scripts/test-install.py
 

.github/workflows/deploy.yaml

@@ -11,6 +11,10 @@ defaults:
 jobs:
   deploy-pypi:
     name: Deploy to PyPI
+    # Having an environment for deployment is strongly recommend by PyPI
+    # https://docs.pypi.org/trusted-publishers/adding-a-publisher/#github-actions
+    # You can comment this line out if you don't want it.
+    environment: deploy
     runs-on: ubuntu-latest
     permissions:
       # this permission is mandatory for trusted publishing with PyPI

.gitignore

@@ -1,10 +1,28 @@
+# Notebooks
+*.ipynb
+
+# Auto-generated docs and helper files
+docs/api/*
+!docs/api/.gitkeep
+docs/cli/*
+!docs/cli/.gitkeep
+
 # pdm stuff
 .pdm-python
 
-# CI stuff
-pdm-install-flags.txt
+# Databases
+*.db
+
+# Jupyter cache
+.jupyter_cache
 
-# licence check
+# IDE stuff
+.idea/
+
+# Ruff cache
+.ruff_cache
+
+# Licence check
 licence-check.txt
 
 # Byte-compiled / optimized / DLL files
@@ -136,3 +154,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Mac stuff
+*.DS_Store

.pre-commit-config.yaml

@@ -3,14 +3,13 @@ ci:
   autofix_prs: false
   autoupdate_schedule: quarterly
   autoupdate_branch: pre-commit-autoupdate
-  # Skip steps that won't run on pre-commit CI for various reasons,
-  # mostly because they rely on local things.
-  skip: [ ]
+  # Currently network access isn't supported in the pre-commit CI product.
+  skip: [pdm-lock-check, pdm-export, pdm-sync]
 
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.5.0'
+    rev: "v4.5.0"
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -34,7 +33,7 @@ repos:
         language: fail
         files: "\\.rej$"
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.1.8'
+    rev: "v0.1.8"
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
@@ -43,10 +42,15 @@ repos:
     rev: 2.17.0
     hooks:
       # Check that the lock file is up to date.
+      # We need the pdm lock file too
+      # so that we can build locked version of the package.
       - id: pdm-lock-check
-        args: [ --dev, --group, ":all" ]
-      # Put a requirements.txt file in the repo too
+        args: ["--dev", "-G", ":all", "--strategy", "inherit_metadata" ]
+      # Put requirements.txt files in the repo too
       - id: pdm-export
-        args: ['--prod', '-o', 'requirements.txt', '--without-hashes']
+        name: export-requirements
+        args: ["-o", "requirements-locked.txt", "--without-hashes", "--prod"]
+      - id: pdm-export
+        name: export-requirements-docs
+        args: ["-o", "requirements-docs-locked.txt", "--without-hashes", "-G", ":all", "-G", "docs"]
       - id: pdm-sync
-        args: [ -G, ":all" ]

.readthedocs.yml → .readthedocs.yaml

@@ -2,8 +2,6 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Thank you also https://browniebroke.com/blog/specify-docs-dependency-groups-with-poetry-and-read-the-docs/
-
 # Required
 version: 2
 
@@ -13,13 +11,10 @@ build:
   tools:
     python: "3.11"
   jobs:
-    post_create_environment:
-      - pip install pdm
     post_install:
-      # RtD seems to be not happy with poetry installs,
+      # RtD seems to be not happy with pdm installs,
       # hence use pip directly instead.
-      - pdm export -f requirements --output requirements.txt --with docs
-      - python -m pip install -r requirements.txt
+      - python -m pip install -r requirements-docs-locked.txt
       - python -m pip list
     pre_build:
       - pip install --no-deps .

Makefile

@@ -32,24 +32,30 @@ checks:  ## run all the linting checks of the codebase
 ruff-fixes:  ## fix the code using ruff
     # format before and after checking so that the formatted stuff is checked and
     # the fixed stuff is formatted
-	pdm run ruff format src tests scripts
-	pdm run ruff check src tests scripts --fix
-	pdm run ruff format src tests scripts
+	pdm run ruff format src tests scripts docs
+	pdm run ruff check src tests scripts docs --fix
+	pdm run ruff format src tests scripts docs
 
 
 .PHONY: test
 test:  ## run the tests
 	pdm run pytest src tests -r a -v --doctest-modules --cov=src
 
 # Note on code coverage and testing:
-# You must specify cov=src as otherwise funny things happen when doctests are
-# involved.
-# If you want to debug what is going on with coverage, we have found
-# that adding COVERAGE_DEBUG=trace to the front of the above command
-# can be very helpful as it shows you if coverage is tracking the coverage
+# You must specify cov=src.
+# Otherwise, funny things happen when doctests are involved.
+# If you want to debug what is going on with coverage,
+# we have found that adding COVERAGE_DEBUG=trace
+# to the front of the below command
+# can be very helpful as it shows you
+# if coverage is tracking the coverage
 # of all of the expected files or not.
-# We are sure that the coverage maintainers would appreciate a PR that improves
-# the coverage handling when there are doctests and a `src` layout like ours.
+# We are sure that the coverage maintainers would appreciate a PR
+# that improves the coverage handling when there are doctests
+# and a `src` layout like ours.
+
+docs/cli/index.md: src/openscm_zenodo/cli/__init__.py  ## auto-generate the typer app docs
+	pdm run typer openscm_zenodo.cli utils docs --output docs/cli/index.md --name openscm-zenodo
 
 .PHONY: docs
 docs: docs/cli/index.md  ## build the docs
@@ -63,22 +69,20 @@ docs-strict: docs/cli/index.md  ## build the docs strictly (e.g. raise an error
 docs-serve: docs/cli/index.md  ## serve the docs locally
 	pdm run mkdocs serve
 
-docs/cli/index.md: src/openscm_zenodo/cli/__init__.py  ## auto-generate the typer app docs
-	pdm run typer openscm_zenodo.cli utils docs --output docs/cli/index.md --name openscm-zenodo
-
 .PHONY: changelog-draft
 changelog-draft:  ## compile a draft of the next changelog
-	pdm run towncrier build --draft
+	pdm run towncrier build --draft --version draft
 
 .PHONY: licence-check
 licence-check:  ## Check that licences of the dependencies are suitable
 	# Will likely fail on Windows, but Makefiles are in general not Windows
 	# compatible so we're not too worried
-	pdm export -o $(TEMP_FILE) --without=tests --without=docs --without=dev
+	pdm export --without=tests --without=docs --without=dev > $(TEMP_FILE)
 	pdm run liccheck -r $(TEMP_FILE) -R licence-check.txt
-	rm $(TEMP_FILE)
+	rm -f $(TEMP_FILE)
 
 .PHONY: virtual-environment
 virtual-environment:  ## update virtual environment, create a new one if it doesn't already exist
-	pdm install -G :all
+	pdm lock --dev --group :all --strategy inherit_metadata
+	pdm install --dev --group :all
 	pdm run pre-commit install