roms-tools 3.1.0__tar.gz → 3.1.2__tar.gz

roms_tools-3.1.2/.github/workflows/close_jira_ticket.yaml

@@ -0,0 +1,56 @@
+name: Close Jira Ticket on Issue Close
+
+on:
+  issues:
+    types: [closed]
+
+jobs:
+  close-jira-ticket:
+    runs-on: ubuntu-latest
+    if: contains(github.event.issue.labels.*.name, 'jira-story')
+    steps:
+      - name: Extract Jira Story Key from Issue Comment
+        id: extract_story_key
+        uses: actions/github-script@v6
+        with:
+          script: |
+            // Fetch all comments on the closed issue
+            const { data: comments } = await github.rest.issues.listComments({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number
+            });
+
+            // Find the comment containing the Jira link
+            const jiraComment = comments.find(comment => comment.body.includes('This issue has been linked to Jira story'));
+            if (!jiraComment) {
+              core.setFailed("No Jira comment found with story key.");
+              return;
+            }
+
+            // Extract the Jira story key from the comment
+            const match = jiraComment.body.match(/\[(.*?)\]\(https:\/\/cworthy\.atlassian\.net\/browse\/.*?\)/);
+            if (!match || match.length < 2) {
+              core.setFailed("Jira story key not found in the comment.");
+              return;
+            }
+            const storyKey = match[1];
+
+            // Print the extracted story key
+            console.log("Extracted STORY_KEY:", storyKey);
+
+            core.setOutput("story_key", storyKey);
+
+      - name: Close Jira Ticket
+        env:
+          JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN_MENDOCINO }}
+          JIRA_EMAIL: ${{ secrets.JIRA_EMAIL_MENDOCINO }}
+          STORY_KEY: ${{ steps.extract_story_key.outputs.story_key }}
+        run: |
+          story_key="${{ steps.extract_story_key.outputs.story_key }}"
+          jira_domain="https://cworthy.atlassian.net"
+
+          curl -s -w "%{http_code}" -o response.json -X POST -u "$JIRA_EMAIL:$JIRA_API_TOKEN" \
+            -H "Content-Type: application/json" \
+            --data '{"transition": {"id": "31"}}' \
+            "$jira_domain/rest/api/3/issue/$story_key/transitions"

roms_tools-3.1.2/.github/workflows/create_jira_tickets.sh

@@ -0,0 +1,188 @@
+#!/bin/bash
+
+######################################
+# FORMAT THE TICKET SUMMARY:
+
+# Escape double quotes in ISSUE_TITLE
+ESCAPED_TITLE="${ISSUE_TITLE//\"/\\\"}"
+
+##############################
+# FORMAT THE TICKET DESCRIPTION:
+
+## Escape double quotes and newlines in ISSUE_BODY
+ESCAPED_BODY="${ISSUE_BODY//\"/\\\"}"
+
+## This is literally the only way to replace newlines with spaces that the Jira API accepts:
+IFS=' ' read -r -d '' ESCAPED_BODY <<<"$ESCAPED_BODY"
+
+## Add link back to original GitHub URL
+ESCAPED_BODY="${ESCAPED_BODY} --- [View the original GitHub issue|$GITHUB_ISSUE_URL]"
+
+##############################
+# DETERMINE ASSIGNEES
+
+# Trim and set GITHUB_ASSIGNEE_USERNAME if needed
+GITHUB_ASSIGNEE_USERNAME=$(echo "$GITHUB_ASSIGNEE_USERNAME" | xargs)
+
+
+# Get the current active sprint for our board
+RESPONSE=$(curl -s -w "%{http_code}" -o sprint_response.json -u "$JIRA_EMAIL_MENDOCINO:$JIRA_API_TOKEN_MENDOCINO" \
+  -H "Content-Type: application/json" \
+  -X GET \
+  "https://cworthy.atlassian.net/rest/agile/1.0/board/$JIRA_BOARD_ID/sprint?state=active")
+
+echo "Jira response (Code $RESPONSE):"
+cat sprint_response.json
+
+ACTIVE_SPRINT_ID=$(jq ".values.[0].id" < sprint_response.json)
+
+
+##############################
+# CREATE THE STORY
+
+# note that customfield_10020 is our sprint field
+# one could figure that out again someday by searching through the results of their GET issue fields endpoint
+
+# Create the JSON payload, adding assignee if there is one
+if [[ -n "$GITHUB_ASSIGNEE_USERNAME" ]]; then
+  # Map GitHub username to Jira account ID
+  JIRA_ASSIGNEE_ID=$(echo "$JIRA_USERID_MAP" | jq ".$GITHUB_ASSIGNEE_USERNAME" | tr -d '"')
+  cat > payload.json <<EOF
+{
+  "fields": {
+    "project": { "key": "$JIRA_BOARD_KEY" },
+    "summary": "$ESCAPED_TITLE",
+    "description": "$ESCAPED_BODY",
+    "issuetype": { "name": "Story" },
+    "assignee": { "accountId": "$JIRA_ASSIGNEE_ID" },
+    "$JIRA_SPRINT_FIELD_ID": $ACTIVE_SPRINT_ID
+  }
+}
+EOF
+else
+  cat > payload.json <<EOF
+{
+  "fields": {
+    "project": { "key": "$JIRA_BOARD_KEY" },
+    "summary": "$ESCAPED_TITLE",
+    "description": "$ESCAPED_BODY",
+    "issuetype": { "name": "Story" },
+    "$JIRA_SPRINT_FIELD_ID": $ACTIVE_SPRINT_ID
+  }
+}
+EOF
+fi
+
+# Display the JSON content for verification
+echo "Generated JSON payload:"
+cat payload.json
+
+# Make the API request to create the main story
+RESPONSE=$(curl -s -w "%{http_code}" -o response.json -X POST -u "$JIRA_EMAIL_MENDOCINO:$JIRA_API_TOKEN_MENDOCINO" \
+  -H "Content-Type: application/json" \
+  -d @payload.json \
+  "https://cworthy.atlassian.net/rest/api/2/issue")
+
+echo "Jira response (Code $RESPONSE):"
+cat response.json
+
+# Check if curl was successful
+if [[ $? -ne 0 || "$RESPONSE" -ne 201 ]]; then
+    echo "Error: Failed to make a request to Jira API."
+  exit 1
+fi
+
+##############################
+# FORMAT SUBTASKS:
+
+# Extract the ID of the story created above
+STORY_ID=$(jq -r '.key' response.json)
+
+# Verify STORY_ID is not empty
+if [[ -z "$STORY_ID" ]]; then
+  echo "Error: STORY_ID is empty. Failed to retrieve a valid story ID."
+  exit 1
+fi
+
+# Use readarray to populate TASKS array directly from matching lines in ISSUE_BODY
+readarray -t TASKS < <(echo "$ISSUE_BODY" | grep -E '^- \[[ x]\] ')
+
+# If there are tasks, create subtasks
+if [[ ${#TASKS[@]} -gt 0 ]]; then
+  echo "Creating subtasks for tasks found in the issue..."
+
+  for TASK in "${TASKS[@]}"; do
+    # Remove the `- [ ]` or `- [x]` prefix from each TASK
+    CLEANED_TASK=$(echo "$TASK" | sed 's/^- \[[ x]\] //')
+
+    # Check for presence of colon and split based on that
+    if [[ "$CLEANED_TASK" == *:* ]]; then
+      # Split into summary and description based on the first colon
+      TASK_SUMMARY="${CLEANED_TASK%%:*}"
+      TASK_DESCRIPTION="${CLEANED_TASK#*:}"
+    else
+      # If no colon, treat the whole line as the summary and leave description empty
+      TASK_SUMMARY="$CLEANED_TASK"
+      TASK_DESCRIPTION=""
+    fi
+
+
+    ## Trim any extra whitespace or newlines in summary and description
+    TASK_SUMMARY=$(echo "$TASK_SUMMARY" | tr -d '\n' | tr -d '\r' | xargs)
+    TASK_DESCRIPTION=$(echo "$TASK_DESCRIPTION" | tr -d '\n' | tr -d '\r' | xargs)
+
+    ## Escape double quotes in the summary and description
+    ESCAPED_TASK_SUMMARY="${TASK_SUMMARY//\"/\\\"}"
+    ESCAPED_TASK_DESCRIPTION="${TASK_DESCRIPTION//\"/\\\"}"
+    ESCAPED_TASK_SUMMARY="${ESCAPED_TASK_SUMMARY//$'\n'/ }"
+    ESCAPED_TASK_DESCRIPTION="${ESCAPED_TASK_DESCRIPTION//$'\n'/ }"
+
+    # Create JSON payload for each subtask with summary and description
+    if [[ -n "$JIRA_ASSIGNEE_ID" ]]; then
+	cat > subtask.json <<EOF
+{
+  "fields": {
+    "project": { "key": "$JIRA_BOARD_KEY" },
+    "summary": "$ESCAPED_TASK_SUMMARY",
+    "description": "$ESCAPED_TASK_DESCRIPTION",
+    "issuetype": { "id": "$JIRA_SUBTASK_ISSUETYPE_ID" },
+    "parent": { "key": "$STORY_ID" },
+    "assignee": { "accountId": "$JIRA_ASSIGNEE_ID" }
+  }
+}
+EOF
+    else
+	cat > subtask.json <<EOF
+{
+  "fields": {
+    "project": { "key": "$JIRA_BOARD_KEY" },
+    "summary": "$ESCAPED_TASK_SUMMARY",
+    "description": "$ESCAPED_TASK_DESCRIPTION",
+    "issuetype": { "id": "$JIRA_SUBTASK_ISSUETYPE_ID" },
+    "parent": { "key": "$STORY_ID" }
+  }
+}
+EOF
+    fi
+    echo "Generated JSON payload for subtask:"
+    cat subtask.json
+
+    # Make the API request to create each subtask
+    SUBTASK_RESPONSE=$(curl -s -w "%{http_code}" -o subtask_response.json -X POST -u "$JIRA_EMAIL_MENDOCINO:$JIRA_API_TOKEN_MENDOCINO" \
+      -H "Content-Type: application/json" \
+      -d @subtask.json \
+      "https://cworthy.atlassian.net/rest/api/2/issue")
+
+    # Check if subtask creation was successful
+    if [[ $? -ne 0 || "$SUBTASK_RESPONSE" -ne 201 ]]; then
+      echo "Error: Failed to create subtask for '$TASK_SUMMARY'. Response:"
+      cat subtask_response.json
+      exit 1
+    else
+      echo "Subtask created successfully for '$TASK_SUMMARY'."
+      cat subtask_response.json
+    fi
+  done
+else
+  echo "No tasks found in the issue body. No subtasks created."
+fi

roms_tools-3.1.2/.github/workflows/open_jira_ticket.yaml

@@ -0,0 +1,39 @@
+name: Create Jira Ticket on Label
+
+on:
+  issues:
+    types: [labeled]
+
+jobs:
+  create_jira_ticket:
+    if: contains(github.event.label.name, 'jira-story')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Run Jira Ticket Creation Script
+        env:
+          JIRA_EMAIL_MENDOCINO: ${{ secrets.JIRA_EMAIL_MENDOCINO }}
+          JIRA_API_TOKEN_MENDOCINO: ${{ secrets.JIRA_API_TOKEN_MENDOCINO }}
+          JIRA_BOARD_ID: ${{ vars.JIRA_BOARD_ID }}
+          JIRA_BOARD_KEY: ${{ vars.JIRA_BOARD_KEY }}
+          JIRA_USERID_MAP: ${{ vars.JIRA_USERID_MAP }}
+          JIRA_SPRINT_FIELD_ID: ${{ vars.JIRA_SPRINT_FIELD_ID }}
+          JIRA_SUBTASK_ISSUETYPE_ID: ${{ vars.JIRA_SUBTASK_ISSUETYPE_ID }}
+          ISSUE_TITLE: "${{ github.event.issue.title }}"
+          ISSUE_BODY: "${{ github.event.issue.body }}"
+          GITHUB_ISSUE_URL: "https://github.com/${{ github.repository }}/issues/${{ github.event.issue.number }}"
+          GITHUB_ASSIGNEE_USERNAME: "${{ github.event.issue.assignee.login }}"
+        run: |
+          .github/workflows/create_jira_tickets.sh
+          STORY_KEY=$(jq -r '.key' response.json)
+          echo "STORY_KEY=$STORY_KEY" >> $GITHUB_ENV
+      - name: Comment on GitHub Issue
+        run: |
+          # Comment on the GitHub issue with the Jira story key
+          COMMENT_BODY="This issue has been linked to Jira story [$STORY_KEY](https://cworthy.atlassian.net/browse/$STORY_KEY)."
+          curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+          -H "Accept: application/vnd.github.v3+json" \
+          -d "{\"body\": \"$COMMENT_BODY\"}" \
+          "https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/comments"

{roms_tools-3.1.0 → roms_tools-3.1.2}/.github/workflows/sphinx.yaml

@@ -11,7 +11,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           cache-downloads: true
           cache-environment: true

{roms_tools-3.1.0 → roms_tools-3.1.2}/.github/workflows/tests.yaml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           cache-downloads: true
           cache-environment: true
@@ -27,7 +27,7 @@ jobs:
           environment-file: ci/environment.yml
           create-args: |
             python=${{ matrix.python-version }}
-          cache-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
+          cache-environment-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
 
       - name: Conda info
         run: conda info
@@ -54,7 +54,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           cache-downloads: true
           cache-environment: true
@@ -62,7 +62,7 @@ jobs:
           environment-file: ci/environment.yml
           create-args: |
             python=${{ matrix.python-version }}
-          cache-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
+          cache-environment-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
 
       - name: Conda info
         run: conda info
@@ -89,7 +89,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           cache-downloads: true
           cache-environment: true
@@ -97,7 +97,7 @@ jobs:
           environment-file: ci/environment.yml
           create-args: |
             python=${{ matrix.python-version }}
-          cache-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
+          cache-environment-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
 
       - name: Conda info
         run: conda info
@@ -110,9 +110,13 @@ jobs:
 
       - name: Running Tests with Streaming
         shell: bash -l {0}
+        env:
+          COPERNICUSMARINE_SERVICE_USERNAME: ${{ secrets.COPERNICUSMARINE_SERVICE_USERNAME }}
+          COPERNICUSMARINE_SERVICE_PASSWORD: ${{ secrets.COPERNICUSMARINE_SERVICE_PASSWORD }}
         run: |
            python -V
-           coverage run --rcfile=coverage.toml -m pytest -m stream --stream --use_dask --verbose roms_tools/tests/*
+           copernicusmarine login
+           coverage run --rcfile=coverage.toml -m pytest -m stream --stream --use_dask --use_gcsfs --use_copernicus --verbose roms_tools/tests/*
 
   test-with-dask-and-xesmf:
     name: 3.13-build-with-dask-and-xesmf
@@ -124,7 +128,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           cache-downloads: true
           cache-environment: true
@@ -132,7 +136,7 @@ jobs:
           environment-file: ci/environment-with-xesmf.yml
           create-args: |
             python=${{ matrix.python-version }}
-          cache-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
+          cache-environment-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
 
       - name: Conda info
         run: conda info

{roms_tools-3.1.0/roms_tools.egg-info → roms_tools-3.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: roms-tools
-Version: 3.1.0
+Version: 3.1.2
 Summary: Tools for running and analysing UCLA-ROMS simulations
 Author-email: Nora Loose <nora.loose@gmail.com>, Thomas Nicholas <tom@cworthy.org>, Scott Eilerman <scott.eilerman@cworthy.org>
 License: Apache-2
@@ -18,7 +18,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: xarray>=2022.6.0
+Requires-Dist: xarray<2025.8.0,>=2022.6.0
 Requires-Dist: numpy<2.3,>2.0
 Requires-Dist: pooch
 Requires-Dist: matplotlib
@@ -31,14 +31,17 @@ Requires-Dist: PyYAML
 Requires-Dist: pyamg
 Requires-Dist: bottleneck
 Requires-Dist: regionmask
-Requires-Dist: xgcm
+Requires-Dist: xgcm>=0.9.0
 Requires-Dist: numba>=0.61.2
 Requires-Dist: pydantic<3,>2
 Provides-Extra: dask
 Requires-Dist: dask[diagnostics]; extra == "dask"
+Requires-Dist: zarr; extra == "dask"
 Provides-Extra: stream
 Requires-Dist: dask[diagnostics]; extra == "stream"
 Requires-Dist: gcsfs; extra == "stream"
+Requires-Dist: zarr; extra == "stream"
+Requires-Dist: copernicusmarine; extra == "stream"
 Dynamic: license-file
 
 # ROMS-Tools