Modernize project infrastructure and switching to hatch (#108)

* Switch to src project structure

* Prevent CI being run twice on PR

Having CI jobs run on PR and push without any further restrictions runs
the CI jobs twice on a new PR, with this setting the CI is only run on
pushes to main.

* Ignore QbFields warning in sphinx

Bug that appeears with aiida 2.6 (independent of this PR), it also goes
away when building the docs twice. For now I ignore it.

* Remove outdated install_aiida_github.sh

It is nowhere used and I am not sure in which context it should be used.
Installing aiida-core seems trivial. What would be useful is something
for creating new profiles in the tests.

* Split pre-commit hook fmt into lint and format

* Change ruff settings single quotes -> double quotes

double quotes are default so nothing has to be changed

* Apply the formatting to double quotes on template repo

* Move docs to an optional dependency for readthedocs

Because readthedocs can only use extra dependencies from the
pyproject.toml, we move the deps of docs into one, so we can reference
it in the readthedocs.yaml

* Updates in the update-aiida-diff.sh script

- Remove `git init` in update aiida-diff script to base on current version
- Remove `hatch fmt` at the end since it is done by hook properly
* Fix formatting in the cookiecutter hook

Now `hatch fmt` is executed twice, running it one time did not fix all
isues. Needs to be investigated, if a reviewer has some ideas.

* Add script update-template-formatting.sh that can be used to fix formatting

To apply the formatting on the cookiecutter template the script initiates
a cookiecutter repo instance and applies the formatting on this instance
the changes are diffed and copied back to the template.

* Update update-aiida-diff.sh

Since the cookiecutter hooks is now also performing the formatting,
the pre-commit is not necessary. The git init has been removed since
the repository already exists.

---------

Co-authored-by: Rico Haeuselmann <r.haeuselmann@gmx.ch>

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.12']
         aiida-version: ['stable']
     services:
       postgres:
@@ -31,10 +31,10 @@ jobs:
           - 5672:5672
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -44,7 +44,6 @@ jobs:
         pip install -r requirements.txt
         # Change plugin_name to test we're not specific to "aiida-diff"
         cookiecutter --no-input . plugin_name=${PLUGIN_NAME}
-        pip install -e ${PLUGIN_NAME}[testing]
       env:
         PLUGIN_NAME: aiida-ck
 
@@ -55,17 +54,17 @@ jobs:
         PLUGIN_NAME: aiida-ck
       run: |
         cd ${PLUGIN_NAME}
-        pytest -v
+        hatch test -v
 
   docs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.12"
     - name: Install python dependencies
       env:
         PLUGIN_NAME: aiida-ck
@@ -74,21 +73,22 @@ jobs:
         pip install -r requirements.txt
         # Change plugin_name to test we're not specific to "aiida-diff"
         cookiecutter --no-input . plugin_name=${PLUGIN_NAME}
-        pip install -e ${PLUGIN_NAME}[docs]
     - name: Build docs
       env:
         PLUGIN_NAME: aiida-ck
-      run: cd ${PLUGIN_NAME}/docs && make
+      run: |
+        cd ${PLUGIN_NAME}
+        hatch run docs:build
 
-  pre-commit:
+  static-analysis:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.12"
     - name: Install python dependencies
       env:
         PLUGIN_NAME: aiida-ck
@@ -97,13 +97,9 @@ jobs:
         pip install -r requirements.txt
         # Change plugin_name to test we're not specific to "aiida-diff"
         cookiecutter --no-input . plugin_name=${PLUGIN_NAME}
-        pip install -e ${PLUGIN_NAME}[pre-commit,docs,testing]
-    - name: Run pre-commit
+    - name: Run formatter and linter
       env:
         PLUGIN_NAME: aiida-ck
       run: |
         cd ${PLUGIN_NAME}
-        git init
-        git add -A
-        pre-commit install
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+        hatch fmt

hooks/post_gen_project.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
-if [ -x "$(command -v black)" ]; then
-    echo "Running black on {{ cookiecutter.plugin_name }}"
-    black '../{{ cookiecutter.plugin_name }}/'
+if [ -x "$(command -v hatch)" ]; then
+    echo "Running hatch on {{ cookiecutter.plugin_name }}"
+    # For some reason we need to invoke the formatting twice to be effective
+    hatch fmt || true
+    hatch fmt || true
 else
-    echo "black not found. 'pip install black' to automatically \
+    echo "hatch not found. 'pip install hatch' to automatically \
           run formatter on {{ cookiecutter.plugin_name }}"
 fi
 

requirements.txt

@@ -1,2 +1,2 @@
 cookiecutter
-black==22.12.0
+hatch~=1.12.0

tox.ini

@@ -19,4 +19,4 @@ commands =
     cookiecutter --no-input . plugin_name={env:PLUGIN_NAME}
     git init -b main {env:PLUGIN_NAME}
     cd {env:PLUGIN_NAME} && git add -A
-    pip install -e {env:PLUGIN_NAME}[testing,docs,pre-commit]
+    pip install -e {env:PLUGIN_NAME}

update-aiida-diff.sh

@@ -11,8 +11,3 @@ else
 fi
 
 cookiecutter --no-input -f . version=1.2.0
-pip install -e aiida-diff[docs,pre-commit,testing]
-cd aiida-diff
-git init && git add -A
-pre-commit install
-pre-commit run

update-template-formatting.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+# Creates plugin cutter with unique labels so we can format and then reverses
+# the ids to the cookiecutter identifiers and git apply the diff
+set -e
+
+# clean directory contents if exist (but don't delete .git directory)
+if [ -d aiida-diff ]; then
+  rm -rf cookiecutter_plugin_name
+fi
+cookiecutter --accept-hooks no --no-input -f . plugin_name=cookiecutter_plugin_name module_name=cookiecutter_module_name short_description=cookiecutter_short_description entry_point_prefix=cookiecutter_entry_point_prefix version=0.0.0-dev author=cookiecutter_author year=cookiecutter_year
+
+cd cookiecutter_plugin_name
+git init && git add -A && git commit -am 'init'
+hatch fmt || true
+# takes the diff and applies it on the cookie cutter template
+git diff > patch
+cp patch ..
+cd ..
+# git diff replacements of specified labels with cookiecutter identifiers
+sed -i 's/ a\// a\/\{\{cookiecutter.plugin_name\}\}\//g' patch
+sed -i 's/ b\// b\/\{\{cookiecutter.plugin_name\}\}\//g' patch
+sed -i 's/cookiecutter_plugin_name/\{\{cookiecutter.plugin_name\}\}/g' patch
+sed -i 's/cookiecutter_module_name/\{\{cookiecutter.module_name\}\}/g' patch
+sed -i 's/cookiecutter_entry_point_prefix/\{\{cookiecutter.entry_point_prefix\}\}/g' patch
+sed -i 's/cookiecutter_short_description/\{\{cookiecutter.short_description\}\}/g' patch
+sed -i 's/0\.0\.0-dev/\{\{cookiecutter.version\}\}/g' patch
+sed -i 's/cookiecutter_author/\{\{cookiecutter.author\}\}/g' patch
+sed -i 's/cookiecutter_year/\{\{cookiecutter.year\}\}/g' patch
+git apply --reject --whitespace=fix patch

{{cookiecutter.plugin_name}}/.github/workflows/ci.yml

@@ -1,6 +1,11 @@
 name: ci
 
-on: [push, pull_request]
+on:
+  push:
+    # only pushes to main trigger
+    branches: [main]
+  pull_request:
+    # always triggered
 
 jobs:
 
@@ -9,7 +14,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.12']
         aiida-version: ['stable']
 
     services:
@@ -32,54 +37,49 @@ jobs:
           - 5672:5672
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ '{{ matrix.python-version }}' }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ '{{ matrix.python-version }}' }}
-
-    - name: Install python dependencies
+    - name: Install project manager
       run: |
-        pip install --upgrade pip
-        pip install -e .[testing]
-
+        pip install hatch
     - name: Run test suite
       env:
-        # show timings of tests
         PYTEST_ADDOPTS: "--durations=0"
-      run: pytest --cov {{cookiecutter.module_name}} --cov-append .
+      run: |
+        hatch test --cover
 
   docs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ '{{ matrix.python-version }}' }}
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-    - name: Install python dependencies
+        python-version: ${{ '{{ matrix.python-version }}' }}
+    - name: Install project manager
       run: |
-        pip install --upgrade pip
-        pip install -e .[docs]
+        pip install hatch
     - name: Build docs
-      run: cd docs && make
+      run: |
+        hatch run docs:build
 
-  pre-commit:
+  static-analysis:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ '{{ matrix.python-version }}' }}
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-    - name: Install python dependencies
+        python-version: ${{ '{{ matrix.python-version }}' }}
+    - name: Install project manager
       run: |
-        pip install --upgrade pip
-        pip install -e .[pre-commit,docs,testing]
-    - name: Run pre-commit
+        pip install hatch
+    - name: Run formatter and linter
       run: |
-        pre-commit install
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+        hatch fmt --check

{{cookiecutter.plugin_name}}/.github/workflows/publish-on-pypi.yml

@@ -15,19 +15,19 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v2
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v1
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.12'
 
-    - name: Install flit
+    - name: Install hatch
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flit~=3.4
+        python -m pip install hatch~=1.12.0
 
     - name: Build and publish
       run: |
-        flit publish
+        hatch publish
       env:
-        FLIT_USERNAME: __token__
-        FLIT_PASSWORD:  ${{ '{{ secrets.pypi_token }}' }}
+        HATCH_INDEX_USER: __token__
+        HATCH_INDEX_AUTH:  ${{ '{{ secrets.pypi_token }}' }}

{{cookiecutter.plugin_name}}/.pre-commit-config.yaml

@@ -1,39 +1,13 @@
-# Install pre-commit hooks via:
-# pre-commit install
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  hooks:
-    - id: end-of-file-fixer
-    - id: mixed-line-ending
-    - id: trailing-whitespace
-    - id: check-json
-
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
-  hooks:
-  - id: pyupgrade
-    args: ["--py37-plus"]
-
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-
-- repo: https://github.com/psf/black
-  rev: 22.12.0
-  hooks:
-    - id: black
-
 - repo: local
   hooks:
-  - id: pylint
+  - id: format
+    name: format
+    entry: hatch fmt -f
+    language: system
+    types: [python]
+  - id: lint
+    name: lint
+    entry: hatch fmt -l
     language: system
-    types: [file, python]
-    name: pylint
-    description: "This hook runs the pylint static code analyzer"
-    exclude: &exclude_files >
-      (?x)^(
-          docs/.*|
-      )$
-    entry: pylint
+    types: [python]