Merge pull request #2 from nsidc/tests-and-ci

Tests and ci

.github/workflows/test.yml

@@ -0,0 +1,57 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+# Default to bash in login mode; key to activating conda environment
+# https://github.com/mamba-org/provision-with-micromamba#IMPORTANT
+defaults:
+  run:
+    shell: "bash -l {0}"
+
+jobs:
+  test:
+    name: "Run tests"
+    runs-on: "ubuntu-latest"
+    steps:
+      - name: "Check out repository"
+        uses: "actions/checkout@v3"
+
+      - name: "Install Conda environment"
+        uses: "mamba-org/setup-micromamba@v1"
+        with:
+          environment-file: "conda-lock.yml"
+          # When using a lock-file, we have to set an environment name.
+          environment-name: "seaice_ecdr-ci"
+          cache-environment: true
+          # Increase this key to trigger cache invalidation
+          cache-environment-key: 1
+
+      - name: "Check out pm_icecon repository"
+        uses: "actions/checkout@v3"
+        with:
+          repository: "nsidc/pm_icecon"
+          ref: "update_for_nise_cdr_cetb"
+          path: "pm_icecon"
+
+      - name: "Check out pm_tb_data repository"
+        uses: "actions/checkout@v3"
+        with:
+          repository: "nsidc/pm_tb_data"
+          ref: "main"
+          path: "pm_tb_data"
+
+      # Linter
+      - name: "Run pre-commit tests"
+        run: "pre-commit run --all-files"
+
+      # Unit tests
+      - name: "Run mypy"
+        run: "PYTHONPATH=/home/runner/work/seaice_ecdr/seaice_ecdr/pm_icecon/:/home/runner/work/seaice_ecdr/seaice_ecdr/pm_tb_data/ mypy"
+
+      # Unit tests
+      # - name: "Run unit tests"
+      #   run: "PYTHONPATH=/home/runner/work/seaice_ecdr/seaice_ecdr/pm_icecon/:/home/runner/work/seaice_ecdr/seaice_ecdr/pm_tb_data/ python -m pytest seaice_ecdr/tests/unit/"

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+default_language_version:
+  python: "python3.10"
+
+
+repos:
+
+  - repo: "https://github.com/pre-commit/pre-commit-hooks"
+    rev: "v4.4.0"
+    hooks:
+      - id: "check-added-large-files"
+      - id: "check-vcs-permalinks"
+      - id: "end-of-file-fixer"
+
+  - repo: "https://github.com/charliermarsh/ruff-pre-commit"
+    rev: "v0.0.291"
+    hooks:
+      - id: "ruff"
+        # NOTE: "--exit-non-zero-on-fix" is important for CI to function
+        # correctly!
+        args: ["--fix", "--exit-non-zero-on-fix"]
+
+  - repo: "https://github.com/psf/black"
+    rev: "23.9.1"
+    hooks:
+      - id: "black"
+
+  - repo: "https://github.com/jendrikseipp/vulture"
+    rev: "v2.9.1"
+    hooks:
+      - id: "vulture"

README.md

@@ -1,11 +1,16 @@
-<p align="center">
-  <img alt="NSIDC logo" src="https://nsidc.org/themes/custom/nsidc/logo.svg" width="150" />
+<p float="left" align="center">
+    <img alt="NSIDC logo" src="https://nsidc.org/themes/custom/nsidc/logo.svg" height="150" />
+    <img alt="NOAA@NSIDC logo" src="https://nsidc.org/sites/default/files/images/Logo/noaa_at_nsidc.png" height="150" />
+    <img alt="NASA logo" src="https://gpm.nasa.gov/sites/default/files/document_files/NASA-Logo-Large.png" height="150" />
 </p>
 
+# Enhanced Sea Ice CDR
 
-# Enhanced SeaIce CDR
+Enhanced SeaIce CDR (ECDR) enables the creation of the 12.5km SeaIce CDR.
 
-Enhanced SeaIce CDR enables the creation of the 12.5km SeaIce CDR
+Please note that this repository is a work in progress and breaking changes are
+to be expected. Initial work on this repository is specific to NSIDC's internal
+systems and may not work as expected for external collaborators.
 
 
 ## Level of Support
@@ -17,34 +22,111 @@ See the [LICENSE](GENERAL) for details on permissions and warranties. Please con
 [email protected] for more information.
 
 
-## Requirements
+## Requirements and installation
 
-The ]seaice_ecdr_vm repository](https://bitbucket.org/nsidc/seaice_ecdr_vm/src/main/) provides the NSIDC VM configuration for this project.
+This code relies on the python packages defined in the included
+`environment.yml` file.
 
+Use [conda](https://docs.conda.io/en/latest/) or
+[mamba](https://mamba.readthedocs.io/en/latest/index.html) to install the
+requirements:
 
-## Installation
+```
+$ conda env create
+```
 
-Clone the seaice_ecdr_vm repository and check out appropriate branches of pm_icecon and seaice_ecdr to install this package
+To activate the environment:
 
+```
+$ conda activate pm_tb_data
+```
 
 ## Usage
 
+TODO
+
+## Development/contributing
+
+### For developers at NSIDC
+
+For developers at the NSIDC, the [seaice_ecdr_vm
+repository](https://bitbucket.org/nsidc/seaice_ecdr_vm/src/main/) provides the
+NSIDC VM configuration for this project.
+
 An initial copy of the pm_icecon "cdr" generation can be executed from the VM directory:
 
-~/seaice_ecdr/
+`~/seaice_ecdr/`
 
 using the cli.sh command:
 
+```
 ./scripts/cli.sh bootstrap amsr2 --date 2022-08-01 --hemisphere north --output-dir /tmp/ --resolution 12
+```
+
+### Adding dependencies
+
+To add new dependencies to this project, update the `environment.yml` file with
+the new dependency. Then update your conda environment:
+
+```
+$ mamba env update
+```
+
+Once the conda environment has been updated, lock the environment using `conda-lock`:
+
+```
+$ conda-lock
+```
+
+Commit the changes for the `environment.yml` and the `conda-lock.yml` files.
+
+
+### Running tests/CI
+
+#### Linting / formatting
+This project uses [pre-commit](https://pre-commit.com/) to run pre-commit hooks
+that check and format this project's code for stylistic consistency (using
+`ruff` and `black`) .
+
+The pre-commit configuration for this project can be found in
+`.pre-commit-config.yaml`. Configuration for specific tools (e.g., `mypy`) is
+given in the included `pyproject.toml`.
+
+For more information about using `pre-commit`, please sese the [Scientific
+Python Library Development Guide's section on
+pre-commit](https://learn.scientific-python.org/development/guides/gha-basic/#pre-commit).
+
+To install pre-commit to run checks for each commit you make:
+
+```
+$ pre-commit install
+```
+
+To manually run the pre-commit hooks without a commit:
+
+```
+$ pre-commit run --all-files
+```
+
+#### Running unit tests
+
+Use `pytest` to run unit tests:
+
+```
+$ python -m pytest
+```
 
+#### Type-checking
 
-## Troubleshooting
+Use `mypy` to run static typechecking
 
-No specific troubleshooting suggestions are currently available.
+```
+$ mypy
+```
 
 ## License
 
-See [LICENSE](GENERAL).
+See [LICENSE](LICENSE).
 
 
 ## Code of Conduct
@@ -54,5 +136,5 @@ See [Code of Conduct](CODE_OF_CONDUCT.md).
 
 ## Credit
 
-This content was developed by the National Snow and Ice Data Center with funding from
-multiple sources.
+This software was developed by the National Snow and Ice Data Center with
+funding from NASA and NOAA.

README_dev.txt

@@ -20,4 +20,3 @@ in ~/seaice_ecdr/:
 
    Can generate a sample netCDF file with:
      python seaice_ecdr/tests/integration/gen_ide_sample.py
-