Merge pull request #5 from neutrons/precommit

Modernize the Repo

.github/pull_request_template.md

@@ -0,0 +1,43 @@
+# Description of the changes
+
+# Manual test for the reviewer
+<!-- Instructions for testing here. -->
+
+# Check list for the reviewer
+- [ ] best software practices
+    + [ ] clearly named variables (better to be verbose in variable names)
+    + [ ] code comments explaining the intent of code blocks
+- [ ] All the tests are passing
+- [ ] The documentation is up to date
+- [ ] code comments added when explaining intent
+
+### Execution of tests requiring the /SNS and /HFIR filesystems
+It is strongly encouraged that the reviewer runs the following tests in their local machine
+because these tests are not run by the GitLab CI. It is assumed that the reviewer has the /SNS and /HFIR filesystems
+remotely mounted in their machine.
+
+```bash
+cd /path/to/my/local/mr_reduction/repo/
+git fetch origin merge-requests/<MERGE_REQUEST_NUMBER>/head:mr<MERGE_REQUEST_NUMBER>
+git switch mr<MERGE_REQUEST_NUMBER>
+conda activate <my_mr_reduction_environment>
+pytest -m mount_eqsans ./tests/unit/ ./tests/integration/
+```
+In the above code snippet, substitute `<MERGE_REQUEST_NUMBER>` for the actual merge request number. Also substitute
+`<my_mr_reduction_environment>` with the name of the conda environment you use for development. It is critical that
+you have installed the repo in editable mode with `pip install -e .` or `conda develop .`
+
+# Check list for the author
+- [ ] I have added tests for my changes
+- [ ] I have updated the documentation accordingly
+- [ ] I ran the tests requiring the /SNS and /HFIR filesystems
+- [ ] I'm including a link to IBM EWM Story or Defect
+
+# Check list for the pull request
+- [ ] source refactored/incremented
+- [ ] tests for my changes
+- [ ] updated the documentation accordingly
+
+# References
+<!-- Links to related issues or pull requests -->
+<!-- Links to IBM EWM items if aaplicable -->

.github/workflows/package.yml

@@ -17,22 +17,20 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          channels: conda-forge,defaults
+          channels: mantid/label/main,conda-forge,defaults
           mamba-version: "*"
           environment-file: environment.yml
           cache-environment-key: ${{ runner.os }}-env-${{ hashFiles('**/environment.yml') }}
           cache-downloads-key: ${{ runner.os }}-downloads-${{ hashFiles('**/environment.yml') }}
-      - name: install additional dependencies
-        run: |
-          echo "installing additional dependencies from environment_development.yml"
       - name: build conda package
         run: |
           # set up environment
           cd conda.recipe
           echo "versioningit $(versioningit ../)"
           # build the package
-          VERSION=$(versioningit ../) conda mambabuild --channel conda-forge --output-folder . .
-          conda verify noarch/mypackagename*.tar.bz2
+          CHANNELS="--channel mantid/label/main --channel conda-forge"
+          VERSION=$(versioningit ../) conda mambabuild $CHANNELS --output-folder . .
+          conda verify noarch/mr_reduction*.tar.bz2
       - name: upload conda package to anaconda
         shell: bash -l {0}
         if: startsWith(github.ref, 'refs/tags/v')
@@ -44,4 +42,4 @@ jobs:
           CONDA_LABEL="main"
           if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
           echo pushing ${{ github.ref }} with label $CONDA_LABEL
-          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/mypackagename*.tar.bz2
+          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/mr_reduction*.tar.bz2

.github/workflows/unittest.yml → .github/workflows/testing.yml

@@ -1,4 +1,4 @@
-name: unit-test
+name: testing
 
 on:
   workflow_dispatch:
@@ -18,7 +18,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          channels: conda-forge,defaults
+          channels: mantid/label/main,conda-forge,defaults
           mamba-version: "*"
           environment-file: environment.yml
           cache-environment-key: ${{ runner.os }}-env-${{ hashFiles('**/environment.yml') }}
@@ -29,18 +29,28 @@ jobs:
       - name: run unit tests
         run: |
           echo "running unit tests"
-          python -m pytest --cov=src --cov-report=xml --cov-report=term-missing tests/
+          python -m pytest -vv -m "not datarepo and not sns_mounted" --cov=src --cov-report=xml --cov-report=term-missing tests/
+          mv .coverage .coverage.unit
+      - name: run integration tests
+        run: |
+          echo "running integration tests"
+          git submodule update --init
+          python -m pytest -vv -m "datarepo" --cov=src --cov-report=xml  --cov-report=term-missing tests/
+          mv .coverage .coverage.integration
+      - name: combine coverage reports
+        run: |
+          coverage combine  # merge all .coverage.* files into .coverage
       - name: upload coverage to codecov
         uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
       - name: build conda package
         run: |
-          # test that the conda package builds
+          # set up environment
           cd conda.recipe
           echo "versioningit $(versioningit ../)"
           # conda channels could have been defined in the conda-incubator, but you can copy/paste the lines
           # below to build the conda package in your local machine
           CHANNELS="--channel mantid/label/main --channel conda-forge"
           VERSION=$(versioningit ../) conda mambabuild $CHANNELS --output-folder . .
-          conda verify noarch/mypackagename*.tar.bz2
+          conda verify noarch/mr_reduction*.tar.bz2

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "tests/mr_reduction-data"]
+	path = tests/mr_reduction-data
+	url = https://code.ornl.gov/sns-hfir-scse/infrastructure/test-data/mr_reduction-data.git

README.md

@@ -1,57 +1,20 @@
-[![codecov](https://codecov.io/gh/neutrons/MagnetismReflectometer/branch/master/graph/badge.svg)](https://codecov.io/gh/neutrons/MagnetismReflectometer)
-
-# MR automated reduction
-Automated reduction code based on Mantid.
-
- - Code under `mr_reduction` is common reduction code.
- - Code under `autoreduce` is the top-level code used by the post-processing.
- - Code under `livereduce` is the top-level code for live reduction.
-
-# Configuration
-The configuration file under `livereduce/livereduce.conf` needs to be place under `/etc` on
-the live reduction node.
-
-# python_project_template
-This repository is a template repository for Python projects under neutrons.
-After you create a new repository using this repo as template, please follow the following steps to adjust it for the new project.
-
-## Codebase Adjustments
-
-1. Adjust the branch protection rules for the new repo. By default, we should protect the `main` (stable), `qa` (release candidate), and `next` (development) branches.
-
-    1.1 Go to the `Settings` tab of the new repo.
+# Magnetism Reflectometer Automated Reduction
+Automated reduction code of magnetic reflectometry data.
 
-    1.2 Click on `Branches` on the left side.
-
-    1.3 Click on `Add rule` button.
-
-    1.4 Follow the instructions from Github.
-
-
-2. Change the License if MIT license is not suitable for you project. For more information about licenses, please
-refer to [Choose an open source license](https://choosealicense.com/).
-
-
-3. Update the environment dependency file `environment.yml`, which contain both runtime and development dependencies.
-For more information about conda environment file, please refer to [Conda environment file](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
-
-    3.1 Specify environment 'name' field to match package name
+<!-- Badges -->
+[![codecov](https://codecov.io/gh/neutrons/MagnetismReflectometer/branch/master/graph/badge.svg)](https://codecov.io/gh/neutrons/MagnetismReflectometer)
 
-    3.2 We strongly recommended using a single `environment.yml` file to manage all the dependencies,
-including the runtime and development dependencies.
 
-    3.3 Please add comments to the `environment.yml` file to explain the dependencies.
+# User
 
-    3.4 Please prune the dependencies to the minimum when possible,
-we would like the solver to figure out the dependency tree for us.
+User guide at [readthedocs](https://mr_reduction.readthedocs.io/en/latest)
 
+# Developer
 
-4. Adjust pre-commit configuration file, `.pre-commit-config.yaml` to enable/disable the hooks you need.
-For more information about pre-commit, please refer to [pre-commit](https://pre-commit.com/).
+Developer documentation at [readthedocs](https://mr_reduction.readthedocs.io/en/latest)
 
+- [contributing to the project](https://mr_reduction.readthedocs.io/en/latest/source/developer/contributing.html)
 
-5. Having code coverage, `codecov.yaml` is **strongly recommended**,
-please refer to [Code coverage](https://coverage.readthedocs.io/en/coverage-5.5/) for more information.
 
 
 6. Adjust the demo Github action yaml files for CI/CD. For more information about Github action,

conda.recipe/meta.yaml

@@ -12,7 +12,7 @@
 {% set build_number = 0 %}
 
 package:
-  name: mypackagename
+  name: mr_reduction
   version: {{ version_number }}
 
 source:
@@ -35,6 +35,15 @@ requirements:
 
   run:
     - python
+    - mantid=6.9.0
+    - numpy
+    - scipy
+    - pandas
+    - plotly
+
+tests:
+  imports:
+    - mr_reduction
 
 about:
   home: {{ url }}