Merge branch 'develop' into domain_variables_cell_measures_coordinates

ioos · Dec 6, 2024 · cee1b39 · cee1b39
2 parents d9ee493 + beef6fb
commit cee1b39
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diff --git a/.github/workflows/cc-plugin-glider-test.yml b/.github/workflows/cc-plugin-glider-test.yml
@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -33,6 +33,6 @@ jobs:
         git clone https://github.com/ioos/cc-plugin-glider.git
         && cd cc-plugin-glider
         && micromamba install --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        && micromamba remove compliance-checker --no-prune --force
+        && micromamba remove compliance-checker --no-prune-deps --force
         && python -m pip install -e . --no-deps --force-reinstall
         && python -m pytest -s -rxs -v cc_plugin_glider
diff --git a/.github/workflows/cc-plugin-ncei-test.yml b/.github/workflows/cc-plugin-ncei-test.yml
@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -33,6 +33,6 @@ jobs:
         git clone https://github.com/ioos/cc-plugin-ncei.git
         && cd cc-plugin-ncei
         && micromamba install --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        && micromamba remove compliance-checker --no-prune --force
+        && micromamba remove compliance-checker --no-prune-deps --force
         && python -m pip install -e . --no-deps --force-reinstall
         && python -m pytest -s -rxs -v cc_plugin_ncei
diff --git a/.github/workflows/cc-plugin-og-test.yml b/.github/workflows/cc-plugin-og-test.yml
@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -33,6 +33,6 @@ jobs:
         git clone https://github.com/uw-farlab/cc-plugin-og.git
         && cd cc-plugin-og
         && micromamba install --file requirements.txt --channel conda-forge
-        && micromamba remove compliance-checker --no-prune --force
+        && micromamba remove compliance-checker --no-prune-deps --force
         && python -m pip install -e . --no-deps --force-reinstall
         && python -m pytest -s -rxs -v cc_plugin_og
diff --git a/.github/workflows/cc-plugin-sgrid-test.yml b/.github/workflows/cc-plugin-sgrid-test.yml
@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -33,6 +33,6 @@ jobs:
         git clone https://github.com/ioos/cc-plugin-sgrid.git
         && cd cc-plugin-sgrid
         && micromamba install --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        && micromamba remove compliance-checker --no-prune --force
+        && micromamba remove compliance-checker --no-prune-deps --force
         && python -m pip install -e . --no-deps --force-reinstall
         && python -m pytest -s -rxs -v cc_plugin_sgrid
diff --git a/.github/workflows/cc-plugin-ugrid-test.yml b/.github/workflows/cc-plugin-ugrid-test.yml
@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -33,6 +33,6 @@ jobs:
         git clone https://github.com/ioos/cc-checker-ugrid.git
         && cd cc-checker-ugrid
         && micromamba install --file requirements.txt --file requirements-dev.txt --channel conda-forge
-        && micromamba remove compliance-checker --no-prune --force
+        && micromamba remove compliance-checker --no-prune-deps --force
         && python -m pip install -e . --no-deps --force-reinstall
         && python -m pytest -s -rxs -v cc_plugin_ugrid
diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -37,6 +37,6 @@ jobs:
       continue-on-error: true
 
     - name: Upload to codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         files: coverage.xml
diff --git a/.github/workflows/default-tests.yml b/.github/workflows/default-tests.yml
@@ -9,13 +9,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        os: [windows-latest, ubuntu-latest, macos-latest]
-        experimental: [false]
-        include:
-          - python-version: "3.12"
-            os: "ubuntu-latest"
-            experimental: true
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
+        os: [ windows-latest, ubuntu-latest, macos-latest ]
       fail-fast: false
     defaults:
       run:
@@ -25,7 +20,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash
@@ -35,11 +30,6 @@ jobs:
           --file test_requirements.txt
           --channel conda-forge
 
-    - name: Install unstable dependencies
-      if: matrix.experimental == true
-      run: |
-        micromamba install conda-forge/label/numpy_dev::numpy
-
     - name: Install compliance-checker
       run: |
         python -m pip install -e . --no-deps --force-reinstall

diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -18,7 +18,7 @@ jobs:
         fetch-depth: 0
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash

diff --git a/.github/workflows/integration-tests.yml b/.github/workflows/integration-tests.yml
@@ -12,7 +12,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-name: TEST
         init-shell: bash

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
     - id: trailing-whitespace
       exclude: compliance_checker/tests/data
@@ -19,7 +19,7 @@ repos:
         - test_requirements.txt
 
 - repo: https://github.com/psf/black
-  rev: 24.4.2
+  rev: 24.10.0
   hooks:
   - id: black
     language_version: python3
@@ -31,21 +31,22 @@ repos:
 
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.5
+  rev: v0.8.1
   hooks:
     - id: ruff
+      args: ["--fix", "--show-fixes"]
 
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: 2.1.3
+  rev: v2.5.0
   hooks:
     - id: pyproject-fmt
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
     - id: codespell
       args:
-        - --ignore-words-list=degreeE,degreee,varn,poit,uint,sur,herat,claus,tung,messsages
+        - --ignore-words-list=degreeE,degreee,varn,poit,uint,sur,herat,claus,tung,messsages,assertin
       exclude: >
           (?x)^(
               .*\.xml|

diff --git a/README.md b/README.md
@@ -22,6 +22,7 @@ It currently supports the following sources and standards:
 | Standard                                                                                                                   | Source                                                            | .nc/OPeNDAP/.cdl | SOS                             |
 | ----------------------------------------------------------------------------------------------------                       | -----------                                                       | ------           | ------------------------------- |
 | [ACDD (1.1, 1.3)](https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery_1-3)                                    | Built-in                                                          | X                | -                               |
+| [CF (1.9)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.9/cf-conventions.html)                            | Built-in                                                          | X                | -                               |
 | [CF (1.8)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html)                            | Built-in                                                          | X                | -                               |
 | [CF (1.7)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html)                            | Built-in                                                          | X                | -                               |
 | [CF (1.6)](http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html)                                             | Built-in                                                          | X                | -                               |
@@ -204,9 +205,10 @@ optional arguments:
 
 ### Check a local file against CF 1.6
 ```
-$ compliance-checker --test=cf:1.6 compliance_checker/tests/data/examples/hycom_global.nc
-
+compliance-checker --test=cf:1.6 compliance_checker/tests/data/examples/hycom_global.nc
+```
 
+```
 --------------------------------------------------------------------------------
                          IOOS Compliance Checker Report
                                   cf:1.6 check
@@ -247,15 +249,15 @@ contains valid packing:                are not of type float or double.
 The remote dataset url is taken from the Data URL section of an OPeNDAP endpoint.
 
 ```shell
-$ compliance-checker --test=acdd:1.3 "http://sos.maracoos.org/stable/dodsC/hrecos/stationHRMARPH-agg.ncml"
+compliance-checker --test=acdd:1.3 "http://sos.maracoos.org/stable/dodsC/hrecos/stationHRMARPH-agg.ncml"
 ```
 
 ### Checking against remote ERDDAP Datasets
 
 ERDDAP datasets are becoming a popular way to access data. Supply an ERDDAP `TableDAP` or `GridDAP` URL to the checker:
 
 ```shell
-$ compliance-checker --test ioos:1.2 "https://pae-paha.pacioos.hawaii.edu/erddap/griddap/pibhmc_bathy_60m_guam"
+compliance-checker --test ioos:1.2 "https://pae-paha.pacioos.hawaii.edu/erddap/griddap/pibhmc_bathy_60m_guam"
 ```
 
 Ensure to supply the URL *without* the format extension at the end (no `.nc`, `.ncCF`, etc.).
@@ -276,37 +278,37 @@ Some examples of ERDDAP datasets:
 ### Write results to text file
 
 ```shell
-$ compliance-checker --test=acdd:1.3 --format=text --output=/tmp/report.txt compliance_checker/tests/data/examples/hycom_global.nc
+compliance-checker --test=acdd:1.3 --format=text --output=/tmp/report.txt compliance_checker/tests/data/examples/hycom_global.nc
 ```
 
 ### Write results to JSON file
 
 ```shell
-$ compliance-checker --test=acdd:1.3 --format=json --output=/tmp/report.json compliance_checker/tests/data/examples/hycom_global.nc
+compliance-checker --test=acdd:1.3 --format=json --output=/tmp/report.json compliance_checker/tests/data/examples/hycom_global.nc
 ```
 
 ### Write results to HTML file
 
 ```shell
-$ compliance-checker --test=acdd:1.3 --format=html --output=/tmp/report.html compliance_checker/tests/data/examples/hycom_global.nc
+compliance-checker --test=acdd:1.3 --format=html --output=/tmp/report.html compliance_checker/tests/data/examples/hycom_global.nc
 ```
 
 ### Output text from multiple input files to one output file
 
 ```
-$ compliance-checker --test=cf:1.6 --format text --output=/tmp/combined_output.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc
+compliance-checker --test=cf:1.6 --format text --output=/tmp/combined_output.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc
 ```
 
 ### Output html and text files from multiple input files (part 1)
 In this case you'll get 2 files ```/tmp/combined_output.txt``` and ```/tmp/combined_output.html``` that contain cf check results for both input files because you only specified 1 output filename.
 ```
-$ compliance-checker --test=cf:1.6 --format text --format html --output=/tmp/combined_output.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc
+compliance-checker --test=cf:1.6 --format text --format html --output=/tmp/combined_output.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc
 ```
 
 ### Output html and text files from multiple input files (part 2)
 In this case you'll get 4 files ```/tmp/hycom.txt```, ```/tmp/hycom.html```, ```/tmp/ww3.txt```, and ```/tmp/ww3.html``` that contain cf check results because you specified as many output filenames as input filenames.
 ```
-$ compliance-checker --test=cf:1.6 --format text --format html --output=/tmp/hycom.txt --output=/tmp/ww3.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc
+compliance-checker --test=cf:1.6 --format text --format html --output=/tmp/hycom.txt --output=/tmp/ww3.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc
 ```
 
 ### Download a particular CF standard names table for use in the test
@@ -317,7 +319,8 @@ During the CF test, if a file has a particular version of the cf standard name t
 try to download the specified version. If it fails, it will fall back to packaged version.
 
 ```
-$ compliance-checker -d 35
+compliance-checker -d 35
+```
 
 Downloading cf-standard-names table version 35 from: http://cfconventions.org/Data/cf-standard-names/35/src/cf-standard-name-table.xml
 ```

diff --git a/cchecker.py b/cchecker.py
@@ -22,21 +22,25 @@ def _print_checker_name_header(checker_str):
 
 def parse_options(opts):
     """
-    Helper function to parse possible options.  Splits option after the first
-    colon to split into key/value pairs.
+    Helper function to parse possible options. Splits option into key/value
+    pairs and optionally a value for the checker option. The separator
+    is a colon.
 
     :param opts: Iterable of strings with options
     :rtype: dict
-    :return: Dictionary with keys as checker type (i.e. "cf", "acdd")
+    :return: Dictionary with keys as checker type (i.e. "cf", "acdd").
+             Each value is a dictionary where keys are checker options and values
+             are checker option values or None if not provided.
     """
-    options_dict = defaultdict(set)
+    options_dict = defaultdict(dict)
     for opt_str in opts:
         try:
-            checker_type, checker_opt = opt_str.split(":", 1)
+            checker_type, checker_opt, *checker_val = opt_str.split(":", 2)
+            checker_val = checker_val[0] if checker_val else None
         except ValueError:
             warnings.warn(f"Could not split option {opt_str}, ignoring", stacklevel=2)
         else:
-            options_dict[checker_type].add(checker_opt)
+            options_dict[checker_type][checker_opt] = checker_val
     return options_dict
 
 
@@ -174,8 +178,9 @@ def main():
                                     checkers.  Multiple options can be specified
                                     via multiple invocations of this switch.
                                     Options should be prefixed with a the
-                                    checker name followed by the option, e.g.
-                                    '<checker>:<option_name>'
+                                    checker name followed by the option,
+                                    potentially followed by a value, e.g.
+                                    '<checker>:<option_name>[:<option_value>]'
 
                                     Available options:
                                     'cf:enable_appendix_a_checks' - Allow check
@@ -235,7 +240,7 @@ def main():
         print(f"IOOS compliance checker version {__version__}")
         sys.exit(0)
 
-    options_dict = parse_options(args.option) if args.option else defaultdict(set)
+    options_dict = parse_options(args.option) if args.option else defaultdict(dict)
 
     if args.describe_checks:
         error_stat = 0

diff --git a/compliance_checker/__init__.py b/compliance_checker/__init__.py
@@ -1,6 +1,7 @@
+from collections.abc import Generator
 from contextlib import contextmanager
 from tempfile import NamedTemporaryFile
-from typing import BinaryIO, Generator
+from typing import BinaryIO
 
 try:
     from ._version import __version__

diff --git a/compliance_checker/base.py b/compliance_checker/base.py
@@ -24,7 +24,7 @@
 
 # Python 3.5+ should work, also have a fallback
 try:
-    from typing import Pattern
+    from re import Pattern
 
     re_pattern_type = Pattern
 except ImportError:
@@ -157,7 +157,7 @@ def setup(self, ds):
     def __init__(self, options=None):
         self._defined_results = defaultdict(lambda: defaultdict(dict))
         if options is None:
-            self.options = set()
+            self.options = {}
         else:
             self.options = options