Merge pull request #9 from sebhmg/GEOPY-1162

GEOPY-1162: review dependencies and CI script in las-geoh5

.github/dependabot.yml

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

.github/workflows/issue_to_jira.yml

@@ -0,0 +1,36 @@
+# This workflow will create a JIRA issue upon creation of a GitHub issue
+
+name: Create JIRA issue
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  new_jira_issue:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: JIRA Login
+      uses: atlassian/[email protected]
+      env:
+        JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
+        JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}
+        JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }}
+    - name: Jira Create issue
+      id: create_jira_issue
+      uses: atlassian/[email protected]
+      with:
+        project: GEOPY
+        issuetype: Story
+        summary: ${{ github.event.issue.title }}
+        description: "_from [GitHub issue #${{ github.event.issue.number }}|${{ github.event.issue.html_url }}]_"
+        # Additional fields in JSON format
+        fields: '{"components": [{"name": "LAS"}]}'
+    - name: Post JIRA link
+      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: ${{ github.event.issue.number }}
+        # The comment body.
+        body: "JIRA issue [${{ steps.create_jira_issue.outputs.issue }}] was created."

.github/workflows/pr_add_jira_summary.yml

@@ -0,0 +1,50 @@
+# This workflow will comment the PR with the JIRA issue summary
+# if a JIRA issue number is detected in the branch name or title
+
+name: Add JIRA issue summary
+
+on:
+  pull_request_target:
+    types: [opened]
+
+jobs:
+  add_jira_summary:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Find JIRA issue key
+      id: find_jira_key
+      env:
+        HEAD_REF: ${{ github.head_ref}}
+        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
+    - name: Get JIRA summary
+      id: get_jira_summary
+      if: ${{ steps.find_jira_key.outputs.issue_key }}
+      env:
+        JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
+        JIRA_BASIC_AUTH: ${{ secrets.JIRA_BASIC_AUTH }}
+      run: >
+        curl -sS -X GET
+        -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
+    - name: Add comment
+      if: ${{ steps.find_jira_key.outputs.issue_key }}
+      env:
+        ISSUE_SUMMARY: ${{ steps.get_jira_summary.outputs.summary }}
+        PR_BODY: ${{ github.event.pull_request.body }}
+      run: >
+        jq
+        --arg ISSUE_ID "${{ steps.find_jira_key.outputs.issue_key }}"
+        --arg ISSUE_SUMMARY "$(cat <<< $ISSUE_SUMMARY)"
+        --arg PR_BODY "$(cat <<< $PR_BODY)"
+        -c '."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_API_URL/repos/$GITHUB_REPOSITORY/pulls/${{ github.event.pull_request.number }}"
+        > /dev/null

.github/workflows/pytest-windows.yml

@@ -71,4 +71,3 @@ jobs:
         uses: codecov/codecov-action@v3
         with:
           name: GitHub
-          token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos

.github/workflows/static-analysis.yml

@@ -24,34 +24,6 @@ env:
   source_dir: las_geoh5
 
 jobs:
-  pre-commit:
-    name: pre-commit
-    strategy:
-      fail-fast: false
-    runs-on: ubuntu-latest
-    env:
-      SKIP: pylint
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
-      - name: capture modified files
-        if: github.event_name == 'pull_request'
-        run: >-
-          git fetch --deepen=500 origin ${{github.base_ref}}
-          && echo "FILES_PARAM=$(
-          git diff --diff-filter=AM --name-only refs/remotes/origin/${{github.base_ref}}... -- | grep -E "^(${source_dir}|tests)/.*\.py$" | xargs
-          )" >> $GITHUB_ENV
-      - name: Run pre-commit on modified files
-        if: github.event_name == 'pull_request' && env.FILES_PARAM
-        uses: pre-commit/[email protected]
-        with:
-          extra_args: --hook-stage push --files ${{ env.FILES_PARAM }}
-      - name: Run pre-commit on all files
-        if: github.event_name == 'push'
-        uses: pre-commit/[email protected]
-        with:
-          extra_args: --hook-stage push --all-files
-
   pylint:
     name: pylint
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -12,18 +12,14 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.10.1
     hooks:
     -   id: black
--   repo: https://github.com/asottile/seed-isort-config
-    rev: v2.2.0
-    hooks:
-    -   id: seed-isort-config
 -   repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
     -   id: isort
-        additional_dependencies: [toml] # to read config from pyproject.toml
+        additional_dependencies: [tomli] # to read config from pyproject.toml
 -   repo: https://github.com/humitos/mirrors-autoflake
     rev: v1.1
     hooks:
@@ -33,17 +29,23 @@ repos:
     hooks:
     -   id: flake8
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.0
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.6.1
     hooks:
     -   id: mypy
-        additional_dependencies: [types-toml]
-        args: [--ignore-missing-imports, --scripts-are-modules, --show-error-context,
-               --show-column-numbers]
+        additional_dependencies: [
+            types-toml,
+            tomli, # to read config from pyproject.toml
+        ]
+-   repo: https://github.com/codingjoe/relint
+    rev: 3.1.0
+    hooks:
+    -   id: relint
+        args: [-W]  # to fail on warnings
 -   repo: local
     hooks:
     -   id: pylint
@@ -57,16 +59,17 @@ repos:
         name: Check copyright
         entry: python devtools/check-copyright.py
         language: python
-        types: [python]
-        exclude: (^setup.py$|(docs|assets)/)
+        files: (^LICENSE|README.rst|\.py|\.pyi)$
+        types: [text]
+        exclude: (^setup.py$|^\.|\b(docs|assets)/)
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
     -   id: codespell
-        exclude: (\.ipynb$|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: v4.5.0
     hooks:
     -   id: trailing-whitespace
         exclude: \.mdj$
@@ -82,11 +85,13 @@ repos:
     -   id: mixed-line-ending
     -   id: name-tests-test
 -   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
     hooks:
     -   id: rst-backticks
+        exclude: ^THIRD_PARTY_SOFTWARE.rst$

.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

pyproject.toml

@@ -9,17 +9,17 @@ python = "^3.9, <3.11"
 
 ## dependencies on github repos
 #geoh5py = { url = "https://github.com/MiraGeoscience/geoh5py/archive/refs/heads/release/0.8.0.zip#sha256=" }
-geoh5py = {version ="~0.8.0rc1", source = "pypi", allow-prereleases = true}
+geoh5py = {version ="~0.8.0rc1", allow-prereleases = true}
 
 ## pip dependencies
-lasio = {version = "~0.31", source = "pypi", allow-prereleases = true}
-tqdm = {version = "^4.64.0"}
+lasio = "~0.31"
+tqdm = "^4.64.0"
 
 [tool.poetry.dev-dependencies]
 pylint = "*"
 pytest = "*"
 pytest-cov = "*"
-toml = "*"
+tomli = "*"
 
 [tool.isort]
 # settings for compatibility between ``isort`` and ``black`` formatting
@@ -28,12 +28,44 @@ include_trailing_comma = true
 force_grid_wrap = 0
 use_parentheses = true
 line_length = 88
-# auto-updated by seed-isort-config
-known_third_party = ["geoh5py", "lasio", "numpy", "pytest", "toml", "tqdm"]
 
 [tool.black]
 # defaults are just fine
 
+[tool.mypy]
+warn_unused_configs = true
+ignore_missing_imports = true
+scripts_are_modules = true
+show_error_context = true
+show_column_numbers = true
+check_untyped_defs = true
+
+plugins = [
+    #    'numpy.typing.mypy_plugin'
+]
+
+[tool.pytest.ini_options]
+addopts = "--cov las_geoh5 --cov-report html --cov-report term-missing:skip-covered"
+
+[tool.coverage.run]
+branch = true
+source = ["las_geoh5"]
+omit = []
+
+[tool.coverage.report]
+exclude_lines = [
+    "raise NotImplementedError",
+    "pass",
+    "if TYPE_CHECKING",
+    "pragma: no cover"
+]
+
+fail_under = 80
+
+[tool.coverage.html]
+skip_empty = true
+skip_covered = true
+
 [build-system]
 requires = ["poetry-core>=1.0.0", "setuptools"]
 build-backend = "poetry.core.masonry.api"

tests/conftest.py

@@ -0,0 +1,21 @@
+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las_geoh5 project.
+#
+#  All rights reserved.
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+import tomli as toml
+
+
+@pytest.fixture
+def pyproject() -> dict:
+    """Return the pyproject.toml as a dictionary."""
+
+    pyproject_path = Path(__file__).resolve().parents[1] / "pyproject.toml"
+    with open(pyproject_path, "rb") as pyproject_file:
+        return toml.load(pyproject_file)

tests/version_test.py

@@ -7,24 +7,12 @@
 from __future__ import annotations
 
 import re
-from pathlib import Path
-
-import toml
 
 import las_geoh5
 
 
-def get_version():
-    path = Path(__file__).resolve().parents[1] / "pyproject.toml"
-
-    with open(str(path), encoding="utf-8") as file:
-        pyproject = toml.loads(file.read())
-
-    return pyproject["tool"]["poetry"]["version"]
-
-
-def test_version_is_consistent():
-    assert las_geoh5.__version__ == get_version()
+def test_version_is_consistent(pyproject: dict):
+    assert las_geoh5.__version__ == pyproject["tool"]["poetry"]["version"]
 
 
 def test_version_is_semver():