Merge pull request #547 from MiraGeoscience/release/0.9.0

GEOPY-1489: merge Release/0.9.0 to main

Author: sebhmg

.codespellignore

@@ -0,0 +1,2 @@
+ba
+nd

.github/dependabot.yml

@@ -9,3 +9,4 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
+    target-branch: "develop"

.github/workflows/issue_to_jira.yml

@@ -28,7 +28,7 @@ jobs:
         # Additional fields in JSON format
         fields: '{"components": [{"name": "geoh5py"}]}'
     - name: Post JIRA link
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         # The number of the issue or pull request in which to create a comment.
         issue-number: ${{ github.event.issue.number }}

.github/workflows/pr_add_jira_summary.yml

@@ -19,7 +19,13 @@ jobs:
         PR_TITLE: ${{ github.event.pull_request.title }}
       run: >
         echo $HEAD_REF $PR_TITLE
-        | echo "issue_key=$(grep -os "\b\(GA\|GEOPY\)-[0-9]\+" | head -n1)" >> $GITHUB_OUTPUT
+        | echo "issue_key=$(
+        grep -osi "\b\(GA\|GEOPY\|DEVOPS\)[ #-]*[0-9]\+"
+        | head -n1
+        | sed -E "s/([A-Z]+)[-# ]*([0-9]+)/\1-\2/i"
+        | tr [:lower:] [:upper:]
+        )"
+        >> $GITHUB_OUTPUT
     - name: Get JIRA summary
       id: get_jira_summary
       if: ${{ steps.find_jira_key.outputs.issue_key }}
@@ -31,18 +37,26 @@ jobs:
         -H "Authorization: Basic $JIRA_BASIC_AUTH"
         -H "Content-Type: application/json"
         "$JIRA_BASE_URL/rest/api/2/issue/${{ steps.find_jira_key.outputs.issue_key }}"
-        | echo "summary=$(jq -r '.fields.summary')" >> $GITHUB_OUTPUT
+        | echo "summary=$(jq -r '.fields.summary // empty')" >> $GITHUB_OUTPUT
+    - name: Extract PR title
+      id: get_pr_title
+      env:
+        PR_TITLE: ${{ github.event.pull_request.title }}
+      run: |
+        echo "text=$(echo $PR_TITLE | sed -E "s/^\s*[?[A-Z]+[-# ]*[0-9]+]?[-: ]*(.*)/\1/i")" >> $GITHUB_OUTPUT
     - name: Add comment
       if: ${{ steps.find_jira_key.outputs.issue_key }}
       env:
         ISSUE_SUMMARY: ${{ steps.get_jira_summary.outputs.summary }}
+        TITLE_TEXT: ${{ steps.get_pr_title.outputs.text }}
         PR_BODY: ${{ github.event.pull_request.body }}
       run: >
         jq
         --arg ISSUE_ID "${{ steps.find_jira_key.outputs.issue_key }}"
         --arg ISSUE_SUMMARY "$(cat <<< $ISSUE_SUMMARY)"
+        --arg TITLE_TEXT "$(cat <<< ${TITLE_TEXT:-$ISSUE_SUMMARY})"
         --arg PR_BODY "$(cat <<< $PR_BODY)"
-        -c '."body"="**" + $ISSUE_ID + " - " + $ISSUE_SUMMARY + "**\n" + $PR_BODY' <<< {}
+        -c '{"title": ($ISSUE_ID + ": " + $TITLE_TEXT), "body": ("**" + $ISSUE_ID + " - " + $ISSUE_SUMMARY + "**\n" + $PR_BODY)}' <<< {}
         | curl -sS -X POST -d @-
         -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}"
         -H "Content-Type: application/json"

.github/workflows/pytest-unix-os.yml

@@ -2,12 +2,7 @@ name: pytest on Unix OS
 
 on:
   pull_request:
-    branches:
-      - develop
-      - main
-      - release/**
-      - feature/**
-      - hotfix/**
+    types: [opened, synchronize, reopened, ready_for_review]
   push:
     branches:
       - develop
@@ -20,16 +15,14 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  source_dir: geoh5py
-
 jobs:
   pytest:
     name: pytest
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:
-        python_ver: ['3.8', '3.9', '3.10']
+        python_ver: ['3.9', '3.10']
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     defaults:
@@ -39,9 +32,9 @@ jobs:
       POETRY_VIRTUALENVS_CREATE: true
       POETRY_VIRTUALENVS_IN_PROJECT: true
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python version
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python_ver }}
       - name: Get full Python version
@@ -52,7 +45,7 @@ jobs:
           curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python -
           echo "$HOME/.poetry/bin" >> $GITHUB_PATH
       - name: Set up cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         env:
           # Increase this value to reset cache if poetry.lock has not changed

.github/workflows/pytest-windows.yml

@@ -2,12 +2,7 @@ name: pytest on Windows
 
 on:
   pull_request:
-    branches:
-      - develop
-      - main
-      - release/**
-      - feature/**
-      - hotfix/**
+    types: [opened, synchronize, reopened, ready_for_review]
   push:
     branches:
       - develop
@@ -20,16 +15,14 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  source_dir: geoh5py
-
 jobs:
   pytest:
     name: pytest (Windows)
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:
-        python_ver: ['3.8', '3.9', '3.10']
+        python_ver: ['3.9', '3.10']
     defaults:
       run:
         shell: bash
@@ -38,9 +31,9 @@ jobs:
       POETRY_VIRTUALENVS_CREATE: true
       POETRY_VIRTUALENVS_IN_PROJECT: true
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python version
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python_ver }}
       - name: Get full Python version
@@ -51,7 +44,7 @@ jobs:
           curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python -
           echo "$HOME/.poetry/bin" >> $GITHUB_PATH
       - name: Set up cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         env:
           # Increase this value to reset cache if poetry.lock has not changed
@@ -68,6 +61,8 @@ jobs:
         run: poetry run pytest --cov --cov-report=xml
       - name: Codecov
         if: ${{ success() && matrix.python_ver == '3.10' }}
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           name: GitHub
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/static-analysis.yml

@@ -2,6 +2,7 @@ name: static analysis
 
 on:
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - develop
       - main
@@ -26,6 +27,7 @@ env:
 jobs:
   pylint:
     name: pylint
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -34,9 +36,9 @@ jobs:
       POETRY_VIRTUALENVS_CREATE: true
       POETRY_VIRTUALENVS_IN_PROJECT: true
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python version
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
       - name: Get full Python version
@@ -48,7 +50,7 @@ jobs:
           curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python -
           echo "$HOME/.poetry/bin" >> $GITHUB_PATH
       - name: Set up cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         env:
           # Increase this value to reset cache if poetry.lock has not changed

.pre-commit-config.yaml

@@ -1,63 +1,63 @@
 
 default_language_version:
     python: python3
-exclude: docs/(conf.py|_ext/)
+exclude: ^docs/(conf.py|_ext/)
 default_stages: [commit,push]
 fail_fast: false
 
 ci:
     skip: [pylint]
+    autoupdate_branch: develop
+    autoupdate_schedule: monthly
 
 repos:
--   repo: https://github.com/psf/black
-    rev: 23.7.0
+-   repo: https://github.com/python-poetry/poetry
+    rev: 1.8.0
     hooks:
-    -   id: black
-        types: [text]
-        types_or: [python, pyi]
+    -   id: poetry-check
+        args: [--lock]
+-   repo: https://github.com/hadialqattan/pycln
+    rev: v2.4.0
+    hooks:
+    -   id: pycln
+        args: [--config=pyproject.toml]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     -   id: isort
         additional_dependencies: [tomli] # to read config from pyproject.toml
-        types: [text]
-        types_or: [python, pyi]
-        exclude: geoh5py/objects/__init__\.py
--   repo: https://github.com/humitos/mirrors-autoflake
-    rev: v1.1
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
     hooks:
-    -   id: autoflake
-        types: [text]
-        types_or: [python, pyi]
+    -   id: black
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
     -   id: flake8
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.2
     hooks:
     -   id: pyupgrade
-        args: [--py37-plus]
+        args: [--py39-plus]
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.10.0
     hooks:
     -   id: mypy
         additional_dependencies: [
-            types-toml,
+#            numpy==1.26.*,  # TODO: fix mypy errors related to numpy
             tomli, # to read config from pyproject.toml
-#            'numpy>=1.23.5,<1.24.0'
+            types-toml,
         ]
         exclude: (geoh5py/interfaces/__init__\.py|geoh5py/handlers/__init__\.py|geoh5py/interfaces|geoh5py/handlers|tests)
 -   repo: https://github.com/codingjoe/relint
-    rev: 3.1.0
+    rev: 3.1.1
     hooks:
     -   id: relint
         args: [-W]  # to fail on warnings
-        exclude: ^setup.py$
 -   repo: local
     hooks:
     -   id: pylint
@@ -67,26 +67,37 @@ repos:
         require_serial: true  # pylint does its own parallelism
         types: [text]
         types_or: [python, pyi]
-        exclude: ^(setup.py$|(devtools|docs|geoh5py/interfaces|geoh5py/handlers)/)
+        exclude: ^(devtools|docs|geoh5py/interfaces|geoh5py/handlers)/
     -   id: check-copyright
         name: Check copyright
         entry: python devtools/check-copyright.py
         language: python
         types: [text]
-        types_or: [python, pyi]
-        exclude: ^(devtools/|docs/|setup.py)
+        files: (^LICENSE|^README(|-dev).rst|\.py|\.pyi)$
+        exclude: (^\.|^docs/)
+    -   id: prepare-commit-msg
+        stages: [prepare-commit-msg]
+        name: Prepare commit message
+        entry: python devtools/git_message_hook.py --prepare
+        language: python
+    -   id: check-commit-msg
+        stages: [commit-msg]
+        name: Check commit message
+        entry: python devtools/git_message_hook.py --check
+        language: python
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
     -   id: codespell
-        exclude: (\.ipynb$|^\.github/workflows/issue_to_jira.yml$)
-        types: [text]
-        types_or: [python, pyi]
+        exclude: (\.lock|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$
+        entry: codespell -I .codespellignore
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
         exclude: \.mdj$
+    -   id: check-json
+        exclude_types: [jupyter]
     -   id: check-toml
     -   id: check-yaml
 #    -   id: check-added-large-files # crashing on some configuration. To be investigated
@@ -95,13 +106,24 @@ repos:
     -   id: debug-statements
     -   id: detect-private-key
     -   id: end-of-file-fixer
-        exclude: \.mdj$
+        exclude: (^\.idea/.*\.xml|\.mdj)$
     -   id: mixed-line-ending
+        exclude: ^\.idea/.*\.xml$
     -   id: name-tests-test
+    -   id: pretty-format-json
+        args:
+            - --autofix
+            - --indent=4
+            - --no-sort-keys
+            - --top-keys
+            - version,title,icon,documentation,conda_environment,run_command,geoh5,monitoring_directory,workspace_geoh5
+        exclude_types: [jupyter]
+        exclude: ^docs/(.*/)?images/
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.2
+    rev: v6.2.0
     hooks:
     -   id: rstcheck
+        exclude: ^THIRD_PARTY_SOFTWARE.rst$
         additional_dependencies: [sphinx]
 -   repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0

README.rst

@@ -57,7 +57,7 @@ Installation
 **geoh5py** is currently written for Python 3.7 or higher, and depends on `NumPy <https://numpy.org/>`_ and
 `h5py <https://www.h5py.org/>`_. Users will likely want to also make use of advanced processing
 techniques made available under the python ecosystem. We therefore recommend installing
-Anaconda to handle the various packages.
+`Miniforge <https://github.com/conda-forge/miniforge#download>`_ `(Windows x86_64) <https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Windows-x86_64.exe>`_ to handle the various packages.
 
 Install **geoh5py** from PyPI::