Merge pull request #59 from MiraGeoscience/release/3.2.0

GEOPY-1489: merge Release/3.2.0 to main

Author: sebhmg

.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": "OMF"}]}'
     - name: Post JIRA link
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v3
       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

@@ -2,6 +2,7 @@ name: pytest on Unix OS
 
 on:
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - develop
       - main
@@ -16,16 +17,14 @@ on:
       - feature/**
       - hotfix/**
 
-env:
-  source_dir: omf
-
 jobs:
   pytest:
     name: pytest (Unix)
+    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]
     runs-on: ${{ matrix.os }}
     defaults:
@@ -62,4 +61,4 @@ jobs:
       - name: Install dependencies
         run: poetry install -vvv
       - name: pytest
-        run: poetry run pytest --cov-report=xml --cov=${source_dir} --cov-branch --cov-fail-under=79
+        run: poetry run pytest --cov --cov-report=xml

.github/workflows/pytest-windows.yml

@@ -2,6 +2,7 @@ name: pytest on Windows
 
 on:
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - develop
       - main
@@ -16,16 +17,14 @@ on:
       - feature/**
       - hotfix/**
 
-env:
-  source_dir: omf
-
 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
@@ -61,9 +60,11 @@ jobs:
       - name: Install dependencies
         run: poetry install -vvv
       - name: pytest
-        run: poetry run pytest --cov-report=xml --cov=${source_dir} --cov-branch --cov-fail-under=79
+        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
@@ -22,6 +23,7 @@ env:
 jobs:
   pylint:
     name: pylint
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     runs-on: ubuntu-latest
     defaults:
       run:

.pre-commit-config.yaml

@@ -1,67 +1,102 @@
 
 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: 23.3.0
+-   repo: https://github.com/python-poetry/poetry
+    rev: 1.8.0
     hooks:
-    -   id: black
+    -   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
--   repo: https://github.com/humitos/mirrors-autoflake
-    rev: v1.1
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
     hooks:
-    -   id: autoflake
+    -   id: black
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
     -   id: flake8
-        files: ^omf/fileio/geoh5*
+        files: ^(omf/fileio/geoh5|tests/)
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.4.0
+    rev: v3.15.2
     hooks:
     -   id: pyupgrade
-        args: [--py38-plus]
+        args: [--py39-plus]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.10.0
     hooks:
     -   id: mypy
-        additional_dependencies: [types-six]
-        args: [--ignore-missing-imports, --scripts-are-modules, --show-error-context,
-               --show-column-numbers]
-        files: ^omf/fileio/geoh5*
+        files: ^(omf/fileio/geoh5|tests/)
+        additional_dependencies: [
+#            numpy==1.26.*,  # TODO: fix mypy errors related to numpy
+            tomli, # to read config from pyproject.toml
+            types-six,
+            types-toml,
+        ]
+        exclude: ^docs/
+-   repo: https://github.com/codingjoe/relint
+    rev: 3.1.1
+    hooks:
+    -   id: relint
+        args: [-W]  # to fail on warnings
+        files: ^omf/fileio/geoh5/
 -   repo: local
     hooks:
     -   id: pylint
         name: pylint
         entry: poetry run pylint
         language: system
         require_serial: true  # pylint does its own parallelism
-        types: [text]
-        types_or: [python, pyi]
-        exclude: (devtools|docs)/
+        types: [python]
         files: ^(omf/fileio/geoh5|tests/)
+#    -   id: check-copyright  # TODO: add missing copyright statements in source files
+#        name: Check copyright
+#        entry: python devtools/check-copyright.py
+#        language: python
+#        types: [text]
+#        exclude: (^\.|^docs/)
+#        files: ^(LICENSE|README(-dev)?.rst|((devtools|omf/fileio/geoh5|tests)/.*\.pyi?))$
+    -   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: v2.2.4
+    rev: v2.2.6
     hooks:
     -   id: codespell
-        exclude: (\.ipynb$|^poetry.lock$)
+        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
@@ -70,13 +105,24 @@ 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

.relint.yml

@@ -0,0 +1,10 @@
+- name: No import os.path
+  pattern: 'from os import\b.*\bpath\b'
+  hint: Use from pathlib import Path
+  filePattern: .*\.pyi?
+  error: false
+- name: No os.path
+  pattern: '\bos\.path\b'
+  hint: Use pathlib.Path
+  filePattern: .*\.pyi?
+  error: false

README.rst

@@ -18,21 +18,13 @@ omf
     :alt: pytest
 
 
-Version: 3.1.0
+Version: 3.2.0
 
 API library for Open Mining Format, a new standard for mining data backed by
 the `Global Mining Standards & Guidelines Group <https://gmggroup.org/>`_.
 
-.. warning::
-    **Pre-Release Notice**
-
-    This is a Beta release of the Open Mining Format (OMF) and the associated
-    Python API. The storage format and libraries might be changed in
-    backward-incompatible ways and are not subject to any SLA or deprecation
-    policy.
 
 .. warning::
-    **Alpha-Release Notice**
 
     This is a fork created by Mira Geoscience for interoperability with the
     geoh5 file format.
@@ -91,3 +83,39 @@ Or from `github <https://github.com/GMSGDataExchange/omf>`_:
     git clone https://github.com/GMSGDataExchange/omf.git
     cd omf
     pip install -e .
+
+
+License
+^^^^^^^
+MIT License
+
+Copyright (c) 2024 Mira Geoscience
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+
+Third Party Software
+^^^^^^^^^^^^^^^^^^^^
+The mira-omf Software may provide links to third party libraries or code (collectively “Third Party Software”)
+to implement various functions. Third Party Software does not comprise part of the Software.
+The use of Third Party Software is governed by the terms of such software license(s).
+Third Party Software notices and/or additional terms and conditions are located in the
+`THIRD_PARTY_SOFTWARE.rst`_ file.
+
+.. _THIRD_PARTY_SOFTWARE.rst: THIRD_PARTY_SOFTWARE.rst