Fix phoenix filter handling

.github/workflows/bump-version.yml

@@ -0,0 +1,108 @@
+name: Bump Version on Release Label
+
+on:
+  pull_request:
+    types: [labeled]
+    branches:
+      - master
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  bump-version:
+    # Run only when a release label is added to an open PR
+    if: |
+      github.event.pull_request.state == 'open' && (
+        github.event.label.name == 'release:major' ||
+        github.event.label.name == 'release:minor' ||
+        github.event.label.name == 'release:patch'
+      )
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out PR branch
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+          fetch-depth: 0
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install tools
+        run: |
+          pip install bump-my-version pandoc
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+          cargo install git-cliff
+
+      - name: Set up Git user
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+
+      - name: Determine version bump type
+        id: bump
+        run: |
+          if [[ "${{ github.event.label.name }}" == "release:major" ]]; then
+            echo "type=major" >> $GITHUB_OUTPUT
+          elif [[ "${{ github.event.label.name }}" == "release:minor" ]]; then
+            echo "type=minor" >> $GITHUB_OUTPUT
+          else
+            echo "type=patch" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Bump version
+        run: bump-my-version bump ${{ steps.bump.outputs.type }}
+        env:
+          BMV_ALLOW_DIRTY: "true"
+
+      - name: Extract version
+        id: version
+        run: |
+          VERSION=$(bump-my-version show current)
+          echo "Extracted version: $VERSION"
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Generate changelog
+        run: |
+          git cliff --unreleased --tag v${{ steps.version.outputs.version }} -o CHANGELOG.md
+          echo "Generated changelog for version ${{ steps.version.outputs.version }}"
+
+      - name: Update HISTORY.rst
+        run: |
+          # Convert CHANGELOG.md to rst and prepend to HISTORY.rst
+          if [ -f CHANGELOG.md ]; then
+            pandoc CHANGELOG.md -f markdown -t rst -o CHANGELOG.rst
+            # Prepend new changelog to HISTORY.rst
+            if [ -f HISTORY.rst ]; then
+              cat CHANGELOG.rst HISTORY.rst > HISTORY_temp.rst
+              mv HISTORY_temp.rst HISTORY.rst
+              echo "Updated HISTORY.rst with version ${{ steps.version.outputs.version }}"
+            else
+              mv CHANGELOG.rst HISTORY.rst
+              echo "Created HISTORY.rst"
+            fi
+          fi
+
+      - name: Commit and push changes to PR branch
+        run: |
+          git add .
+          git commit -m "chore: bump version to ${{ steps.version.outputs.version }} and update changelog [skip ci]" || echo "No changes to commit"
+          git push origin HEAD:${{ github.head_ref }}
+
+      - name: Add comment to PR
+        uses: actions/github-script@v7
+        with:
+          script: |
+            github.rest.issues.createComment({
+              issue_number: context.issue.number,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: '🚀 Version bumped to **v${{ steps.version.outputs.version }}** and changelog updated. Ready to merge!'
+            })

.github/workflows/publish.yml

@@ -1,104 +1,17 @@
-name: Publish on PR merge
+name: Publish to PyPI
 
 on:
   pull_request:
-    types: [opened, synchronize, reopened, labeled, closed]
+    types: [closed]
     branches:
       - master
 
 permissions:
   contents: write
   id-token: write
-  pull-requests: write
 
 jobs:
-  update-version-and-changelog:
-    # Run only when a release label is added (not on every push)
-    if: |
-      github.event.action == 'labeled' &&
-      github.event.pull_request.merged == false && (
-        contains(github.event.pull_request.labels.*.name, 'release:major') ||
-        contains(github.event.pull_request.labels.*.name, 'release:minor') ||
-        contains(github.event.pull_request.labels.*.name, 'release:patch')
-      )
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Check out PR branch
-        uses: actions/checkout@v4
-        with:
-          ref: ${{ github.head_ref }}
-          fetch-depth: 0
-          token: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.13"
-
-      - name: Install tools
-        run: |
-          pip install bump-my-version build pandoc
-          sudo apt-get update
-          sudo apt-get install -y pandoc
-          cargo install git-cliff
-
-      - name: Set up Git user
-        run: |
-          git config --local user.email "github-actions[bot]@users.noreply.github.com"
-          git config --local user.name "github-actions[bot]"
-
-      - name: Determine version bump type
-        id: bump
-        run: |
-          if [[ "${{ contains(github.event.pull_request.labels.*.name, 'release:major') }}" == "true" ]]; then
-            echo "type=major" >> $GITHUB_OUTPUT
-          elif [[ "${{ contains(github.event.pull_request.labels.*.name, 'release:minor') }}" == "true" ]]; then
-            echo "type=minor" >> $GITHUB_OUTPUT
-          else
-            echo "type=patch" >> $GITHUB_OUTPUT
-          fi
-
-      - name: Bump version
-        run: bump-my-version bump ${{ steps.bump.outputs.type }}
-        env:
-          BMV_ALLOW_DIRTY: "true"
-
-      - name: Extract version
-        id: version
-        run: |
-          VERSION=$(bump-my-version show current)
-          echo "Extracted version: $VERSION"
-          echo "version=$VERSION" >> $GITHUB_OUTPUT
-
-      - name: Generate changelog
-        run: |
-          git cliff -o CHANGELOG.md
-          echo "Generated changelog for version ${{ steps.version.outputs.version }}"
-
-      - name: Update HISTORY.rst
-        run: |
-          # Convert CHANGELOG.md to rst and prepend to HISTORY.rst
-          if [ -f CHANGELOG.md ]; then
-            pandoc CHANGELOG.md -f markdown -t rst -o CHANGELOG.rst
-            # Prepend new changelog to HISTORY.rst
-            if [ -f HISTORY.rst ]; then
-              cat HISTORY.rst CHANGELOG.rst > HISTORY_temp.rst
-              mv HISTORY_temp.rst HISTORY.rst
-              echo "Updated HISTORY.rst with version ${{ steps.version.outputs.version }}"
-            else
-              mv CHANGELOG.rst HISTORY.rst
-              echo "Created HISTORY.rst"
-            fi
-          fi
-
-      - name: Commit and push changes to PR branch
-        run: |
-          git add .
-          git commit -m "chore: bump version to ${{ steps.version.outputs.version }} and update changelog [skip ci]" || echo "No changes to commit"
-          git push origin HEAD:${{ github.head_ref }}
-
-  publish-after-merge:
+  publish:
     # Run only after PR is merged with release labels
     if: |
       github.event.pull_request.merged == true && (
@@ -125,7 +38,7 @@ jobs:
       - name: Extract version
         id: version
         run: |
-          VERSION=$(bump-my-version show current)
+          VERSION=$(bump-my-version show current_version)
           echo "version=$VERSION" >> $GITHUB_OUTPUT
 
       - name: Create GitHub Release
@@ -146,7 +59,7 @@ jobs:
           repository-url: https://test.pypi.org/legacy/
           skip-existing: true
           attestations: false
-
+          
       - name: Publish to PyPI
         if: steps.test-pypi.outcome == 'success'
         uses: pypa/gh-action-pypi-publish@v1.13.0

cliff.toml

@@ -1,15 +1,17 @@
 [changelog]
-header = """# Changelog
+header = """
+# Changelog
 
 All notable changes to this project will be documented in this file.
 """
 
 body = """
 {% for group, commits in commits | group_by(attribute="group") %}
-    ## {{ group | upper_first }}
-    {% for commit in commits %}
-        - {% if commit.breaking %}[**BREAKING**] {% endif %}{{ commit.message | upper_first }} ([{{ commit.id | truncate(length=7, end="") }}]({{ commit.id }}))
-    {% endfor %}
+## {{ group | upper_first }}
+{% for commit in commits %}
+- {% if commit.breaking %}[**BREAKING**] {% endif %}{{ commit.message | upper_first }} ([{{ commit.id | truncate(length=7, end="") }}](https://github.com/kujaku11/mth5/commit/{{ commit.id }}))
+{% endfor %}
+
 {% endfor %}
 """
 
@@ -26,11 +28,16 @@ commit_parsers = [
   { message = "^refactor", group = "Refactor" },
   { message = "^style", group = "Styling" },
   { message = "^test", group = "Testing" },
-  { message = "^chore\\(release\\): prepare for", skip = true },
-  { message = "^chore\\(deps\\)", skip = true },
-  { message = "^chore\\(pr\\)", skip = true },
-  { message = "^chore\\(pull\\)", skip = true },
+  { message = "^chore(release): prepare for", skip = true },
+  { message = "^chore(deps)", skip = true },
+  { message = "^chore(pr)", skip = true },
+  { message = "^chore(pull)", skip = true },
+  { message = "^chore|^ci", skip = true },
   { message = "^chore", group = "Miscellaneous Tasks" },
   { body = ".*security", group = "Security" },
   { message = "^revert", group = "Revert" },
 ]
+
+# Skip commits that only bump versions
+filter_commits = true
+skip_tags = "v0.1.0-beta.1"

docs/environment.yml

@@ -10,8 +10,8 @@ dependencies:
   - ipython
   - jupyter_client
   - nbsphinx
+  - setuptools<=70
   - obspy
-  - setuptools
   - sphinx>=2.3
   - sphinx_rtd_theme>=0.4
   - sphinx-autoapi

docs/examples/notebooks/new_documentation.ipynb

@@ -0,0 +1,85 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "3832cec5",
+   "metadata": {},
+   "source": [
+    "# MTH5: Add documentation\n",
+    "\n",
+    "This documentation is for a quick start and put stuff in all the same place.\n",
+    "\n",
+    "## Phoenix\n",
+    "\n",
+    "- Sensor calibration: if a dict is input the values should be validated to be PhoenixCalibration object, if a path is given then it should create a object.   \n",
+    "- Change to have no calibration files. \n",
+    "- station_group.run_summary doesn't work.\n",
+    "- Filters are not being extracted to HDF5\n",
+    "- HDF5 tools don't always work, create some tests to run HDF5 tools\n",
+    "- Start time in older data should come from the file not the metadata file.\n",
+    "\n",
+    "### MTU\n",
+    "\n",
+    "- Doesn't know TS2, need to add.\n",
+    "- Seems like the files for bursts are being overwritten.  \n",
+    "\n",
+    "## Geomagnetic Observatory data\n",
+    "\n",
+    "- Add intermagnetic to clients\n",
+    "- world data center for geomagnetism\n",
+    "\n",
+    "## Metronix \n",
+    "\n",
+    "- Add a .ats reader.  There id documentation on Metronix website.  Check Resistics and Razorback\n",
+    "\n",
+    "## Channel Summary\n",
+    "\n",
+    "- Add column for sensor.id, sensor.manufacturer, data_logger.id, data_logger.manufacturer\n",
+    "\n",
+    "## Metadata\n",
+    "\n",
+    "- station id allow for \"-\" in name.\n",
+    "\n",
+    "## Documentation\n",
+    "\n",
+    "- Add documentation of MakeMTH5\n",
+    "\n",
+    "## LEMI\n",
+    "\n",
+    "- Need ability to input dipole length.  True dipole length and instrument dipole length.  \n",
+    "- put this in the collection and add kwargs as e1, e2, e3, e4.\n",
+    "\n",
+    "## IO Repository\n",
+    "\n",
+    "- Add a repository for file readers IO that has Matlab, C++, Python readers\n",
+    "\n",
+    "## Organization GitHub\n",
+    "\n",
+    "- Add documentation how-to document\n",
+    "- Test data: how-to add data\n",
+    "- Readme: add how-to contribute\n",
+    "\n",
+    "# Release Date\n",
+    "\n",
+    "- Mid-June\n",
+    "\n",
+    "\n",
+    "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d84fbc4f",
+   "metadata": {},
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}