Lint and fix CI

.github/workflows/lint.yml

@@ -10,10 +10,21 @@ jobs:
     if: github.event_name == 'push' || !contains(github.event.pull_request.labels.*.name, 'no_ci')
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - name: "get tags"
+        run: |
+          git fetch --tags --force # Retrieve annotated tags.
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
 
       - name: install linting packages
-        run: pip install pre-commit
+        run: uv tool install pre-commit
 
       - name: run all precommits
-        run: pre-commit run flake8 --files src/**/*
+        run: uv run pre-commit run --all

.github/workflows/on_master_commits.yml

@@ -14,14 +14,23 @@ jobs:
         with:
           fetch-depth: 0  # need this so tags are pulled and versions work
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          miniconda-version: 'latest'
-          python-version: "3.10"
-          activate-environment: test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
+          environment-file: .github/workflows/test_conda_env.yml
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
+
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
+        shell: bash -l {0}
+        run: |
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate test
 
       - name: install obsplus
         shell: bash -l {0}
@@ -58,14 +67,23 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          miniconda-version: 'latest'
-          python-version: "3.9"
-          activate-environment: test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
+          environment-file: .github/workflows/test_conda_env.yml
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
+
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
+        shell: bash -l {0}
+        run: |
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate test
 
       - name: install obsplus
         shell: bash -l {0}

.github/workflows/release_published.yml

@@ -13,19 +13,23 @@ jobs:
         with:
           fetch-depth: 0  # need this so tags are pulled and versions work
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          miniconda-version: 'latest'
-          python-version: "3.10"
-          activate-environment: test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
+          environment-file: .github/workflows/test_conda_env.yml
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
 
-      - name: install obsplus
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
         shell: bash -l {0}
         run: |
-          pip install -e .[dev]
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate test
 
       - name: git config
         shell: bash -l {0}
@@ -54,14 +58,23 @@ jobs:
         with:
           fetch-depth: 0  # need this so tags are pulled and versions work
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          miniconda-version: 'latest'
-          python-version: "3.10"
-          activate-environment: test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
+          environment-file: .github/workflows/test_conda_env.yml
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
+
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
+        shell: bash -l {0}
+        run: |
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate test
 
       - name: install obsplus
         shell: bash -l {0}

.github/workflows/runtests.yml

@@ -48,29 +48,23 @@ jobs:
         with:
           fetch-depth: 0  # need this so tags are pulled and versions work
 
-      - name: Get year week
-        id: date
-        run: echo "date=$(date +'%Y:%U')" >> $GITHUB_STATE
-
-      - name: setup conda env
-        uses: conda-incubator/[email protected]
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: test
-          use-mamba: true
-          python-version: ${{ matrix.python-version }}
-
-      - name: Cache conda env
-        uses: actions/cache@v3
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          path: ${{ env.prefix }}
-          key: ${{ env.cache_key }}-hash${{ hashFiles(env.env_file) }}-${{ steps.date.outputs.date }}-${{ env.CACHE_NUMBER }}
-        id: cache
-
-      - name: Update environment
-        run: mamba env update -n test -f ${{ env.env_file }}
-        if: steps.cache.outputs.cache-hit != 'true'
+          micromamba-version: '1.5.8-0' # versions: https://github.com/mamba-org/micromamba-releases
+          environment-file: .github/workflows/test_conda_env.yml
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          post-cleanup: 'all'
+
+      # Not sure why this is needed but it appears to be the case
+      - name: fix env
+        shell: bash -l {0}
+        run: |
+          micromamba shell init --shell bash --root-prefix=~/micromamba
+          eval "$(micromamba shell hook --shell bash)"
+          micromamba activate test
 
       - name: install obsplus
         shell: bash -l {0}

.pre-commit-config.yaml

@@ -1,30 +1,33 @@
+exclude: scripts/_templates
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
-    -   id: trailing-whitespace
--   repo: https://github.com/psf/black
-    rev: 22.10.0
+    -   id: check-merge-conflict
+    -   id: mixed-line-ending
+        args: ['--fix=lf']
+
+    # Ruff is a replacement for flake8 and many other linters (much faster too)
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.8
     hooks:
-    -   id: black
-        language_version: python3
--   repo: https://github.com/asottile/blacken-docs
-    rev: v1.10.0
+    -   id: ruff
+        args: ["--fix"]
+        # Run the formatter.
+    -   id: ruff-format
+
+    # ensures __future__ import annotations at top of files which require it
+    # for the typing features they are using.
+-   repo: https://github.com/frostming/fix-future-annotations
+    rev: 0.5.0
     hooks:
-    -   id: blacken-docs
-        additional_dependencies: [black==21.5b1]
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-    -   id: flake8
-        additional_dependencies:
-          - flake8-black
-          - flake8-breakpoint
-          - flake8-docstrings
+    -   id: fix-future-annotations
+
+    # strips out all outputs from notebooks.
 -   repo: https://github.com/kynan/nbstripout
-    rev: 0.3.9
+    rev: 0.6.1
     hooks:
     -   id: nbstripout
-        files: ".ipynb"

docs/conf.py

@@ -1,5 +1,7 @@
+"""
+Sphinx configuration for ObsPlus doc build.
+"""
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 #
 # obsplus documentation build configuration file, created by
 # sphinx-quickstart
@@ -15,7 +17,7 @@
 
 import datetime
 import sys
-from os.path import dirname, abspath
+from os.path import abspath, dirname
 
 year = datetime.datetime.now().year
 
@@ -34,7 +36,7 @@
 # version is used.
 sys.path.insert(0, project_root)
 
-import obsplus
+import obsplus  # noqa
 
 # load the datasets used by docs here so notebooks don't have to
 obsplus.load_dataset("crandall_test")

docs/notebooks/datasets/datasets.ipynb

@@ -22,8 +22,10 @@
    "outputs": [],
    "source": [
     "import obspy\n",
+    "\n",
     "import obsplus\n",
-    "ds = obsplus.load_dataset('crandall_test')"
+    "\n",
+    "ds = obsplus.load_dataset(\"crandall_test\")"
    ]
   },
   {
@@ -128,8 +130,8 @@
    "source": [
     "from pathlib import Path\n",
     "\n",
-    "obsplus.copy_dataset('crandall_test', '.')\n",
-    "path = Path('.') / 'crandall_test'\n",
+    "obsplus.copy_dataset(\"crandall_test\", \".\")\n",
+    "path = Path(\".\") / \"crandall_test\"\n",
     "assert path.exists() and path.is_dir()"
    ]
   },
@@ -169,7 +171,7 @@
     "import shutil\n",
     "from pathlib import Path\n",
     "\n",
-    "path = Path('crandall_test')\n",
+    "path = Path(\"crandall_test\")\n",
     "if path.exists():\n",
     "    shutil.rmtree(path)"
    ]

docs/notebooks/datastructures/events_to_pandas.ipynb

@@ -21,10 +21,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import obspy\n",
-    "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
-    "from obspy.clients.fdsn import Client\n",
     "\n",
     "import obsplus"
    ]
@@ -35,7 +32,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "crandall = obsplus.load_dataset('crandall_test')\n",
+    "crandall = obsplus.load_dataset(\"crandall_test\")\n",
     "cat = crandall.event_client.get_events()\n",
     "ev_df = obsplus.events_to_df(cat)\n",
     "\n",
@@ -112,7 +109,7 @@
    "outputs": [],
    "source": [
     "# calculate the max pick_time for each event\n",
-    "picks.groupby('event_id')['time'].max()"
+    "picks.groupby(\"event_id\")[\"time\"].max()"
    ]
   },
   {
@@ -129,20 +126,20 @@
    "outputs": [],
    "source": [
     "# get only P picks\n",
-    "df = picks[picks.phase_hint.str.upper() == 'P']\n",
+    "df = picks[picks.phase_hint.str.upper() == \"P\"]\n",
     "\n",
     "# add columns for travel time\n",
-    "df['travel_time'] = df['time'] - df['event_time']\n",
+    "df[\"travel_time\"] = df[\"time\"] - df[\"event_time\"]\n",
     "\n",
     "# filter out stations that aren't used at least 3 times\n",
-    "station_count = df['station'].value_counts()\n",
+    "station_count = df[\"station\"].value_counts()\n",
     "stations_with_three = station_count[station_count > 2]\n",
     "\n",
     "# only include picks that are used on at least 3 stations\n",
     "df = df[df.station.isin(stations_with_three.index)]\n",
     "\n",
     "# get stats of travel times\n",
-    "df.groupby('station')['travel_time'].describe()"
+    "df.groupby(\"station\")[\"travel_time\"].describe()"
    ]
   },
   {