Merge pull request #56 from MiraGeoscience/release/0.1.0

GEOPY-1489: merge Release/0.1.0 to main

.gitattributes

@@ -1,4 +1,4 @@
 *.pt filter=lfs diff=lfs merge=lfs -text
 *.geoh5 filter=lfs diff=lfs merge=lfs -text
-/assets/** filter=lfs diff=lfs merge=lfs -text
 *.h5 filter=lfs diff=lfs merge=lfs -text
+*.min.js filter=lfs diff=lfs merge=lfs -text

.github/workflows/issue_to_jira.yml

@@ -28,7 +28,7 @@ jobs:
         # Additional fields in JSON format
         fields: '{"components": [{"name": "peak-finder-app"}]}'
     - 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.yaml → .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
@@ -20,35 +21,33 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  source_dir: peak_finder
-
 jobs:
   pytest:
     name: pytest (Unix)
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:
-        python_ver: ['3.9', '3.10']
-        os: [ubuntu-latest, macos-latest]
+        python_ver: ['3.10']
+        os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     env:
       PYTHONUTF8: 1
-      CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.lock.yml
-      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
+      CONDA_CHANNEL_PRIORITY: strict
+      PIP_NO_DEPS: 1 # all dependencies are installed from conda
+      CONDA_LOCK_ENV_FILE: environments/py-${{ matrix.python_ver }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.conda.lock.yml
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
           cache-downloads: true
       - name: pytest
-        run: |
-          pytest --cov=${source_dir} --cov-report=xml --cov-branch
+        run: pytest --cov --cov-report=xml

.github/workflows/pytest-windows.yaml → .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
@@ -20,39 +21,40 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  source_dir: peak_finder
-
 jobs:
   pytest:
     name: pytest (Windows)
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:
-        python_ver: ['3.9', '3.10']
+        python_ver: ['3.10']
     defaults:
       run:
         shell: powershell
     runs-on: windows-latest
     env:
       PYTHONUTF8: 1
-      CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-win-64-dev.lock.yml
-      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
+      CONDA_CHANNEL_PRIORITY: strict
+      PIP_NO_DEPS: 1 # all dependencies are installed from conda
+      CONDA_LOCK_ENV_FILE: environments/py-${{ matrix.python_ver }}-win-64-dev.conda.lock.yml
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
+          init-shell: powershell
           cache-downloads: true
       - name: pytest
-        run: |
-          pytest --cov=${source_dir} --cov-report=xml --cov-branch
+        run: pytest --cov --cov-report=xml
       - name: Codecov
-        if: ${{ success() && matrix.python_ver == '3.9' }}
-        uses: codecov/codecov-action@v3
+        if: ${{ success() && matrix.python_ver == '3.10' }}
+        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
@@ -26,18 +27,20 @@ env:
 jobs:
   pylint:
     name: pylint
-    runs-on: windows-latest
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     env:
       PYTHONUTF8: 1
-      CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-win-64-dev.lock.yml
-      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
+      CONDA_CHANNEL_PRIORITY: strict
+      PIP_NO_DEPS: 1 # all dependencies are installed from conda
+      CONDA_LOCK_ENV_FILE: environments/py-3.10-linux-64-dev.conda.lock.yml
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: linter_env