CI/CD (#59)

* cicd

* try to speed up tests

* cancel previous runs on push

* lower tol for windows

* change name for pypi

* metadata update

* readme updates

.github/workflows/deploy.yml

@@ -0,0 +1,46 @@
+name: deploy
+
+on:
+  workflow_run:
+    branches:
+      - master
+    workflows:
+      - "tests"
+      - "mypy"
+      - "ruff"
+    types: 
+      - completed
+
+jobs:
+  deploy:
+    name: deploy-to-pypi
+    runs-on: ubuntu-latest
+    # only run if previous workflows were a success
+    # AND the commit starts with v (meaning it's a tag)
+    if: ${{ github.event.workflow_run.conclusion == 'success' && startsWith(github.event.workflow_run.head_commit.message, 'v') }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          git tag
+          pip install -U pip
+          pip install -U build twine
+          python -m build
+          twine check dist/*
+          ls -lh dist
+      - name: build and publish
+        run: twine upload dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_KEY }}
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

.github/workflows/lint.yml

@@ -1,6 +1,6 @@
 name: ruff
 
-on: [push]
+on: [pull_request]
 
 jobs:
   build:
@@ -10,6 +10,11 @@ jobs:
         python-version: ["3.11"]
 
     steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
     - name: Checkout
       uses: actions/checkout@v4
 

.github/workflows/mypy.yml

@@ -1,6 +1,6 @@
 name: mypy
 
-on: [push]
+on: [pull_request]
 
 jobs:
   build:
@@ -10,6 +10,11 @@ jobs:
         python-version: ["3.11"]
 
     steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
     - name: Checkout
       uses: actions/checkout@v4
 

.github/workflows/tests.yml

@@ -1,15 +1,30 @@
 name: tests
 
-on: [push]
+on:
+  pull_request:
+  schedule:
+    - cron: "0 12 * * 1" # monday at noon GMT
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    name: ${{ matrix.platform }}
+    runs-on: ${{ matrix.platform }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.11"]
+        python-version:
+          - '3.11'
+        platform:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
 
     steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
     - name: Checkout
       uses: actions/checkout@v4
       with:

README.md

@@ -18,26 +18,23 @@ Map Enhancement Tools for Ephemeral Occupancy Refinement
 
 Finally: a word of caution. Expect changes in the coming weeks as we stress test the code. You might want to consider this before publishing any results with `meteor` until we exit `beta`. 
 
-In that vein, for now please install the current master branch as per the following instructions. We'll have a sane
-first stable version soon, which will be deployed straight to `PyPI` and `conda-forge`. Stay posted.
-
-First, we recommend you make a new environment. For conda users,
+First, meteor needs a `python3.11` environment. We're working hard to extend this to as many versions as possible. To be sure things work, we recommend [installing conda](https://docs.anaconda.com/miniconda/) and creating a fresh environment,
 ```
 conda create --name meteor python==3.11 --yes
 conda activate meteor
 ```
 
-Then install from github,
+Then install `meteor` using pip
 ```
-pip install git+https://github.com/alisiafadini/meteor
+pip install meteor-maps
 ```
 
 Once installed, you will have two command-line scripts. Ask for more info using `-h`:
 ```
 meteor.diffmap -h
 meteor.phaseboost -h
 ```
-which compute denoised difference maps using the constant-phase approximation _vs._ iterative phase retrieval, respectively.
+these scripts compute denoised difference maps using the constant-phase approximation _vs._ iterative phase retrieval, respectively.
 
 
 ## philosophy: better science through automation

pyproject.toml

@@ -3,14 +3,19 @@ requires = ["setuptools >= 61.0", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "meteor"
+name = "meteor-maps"
 description = "denoise crystallographic difference maps"
 dynamic = ["version"]
 authors = [
     { name = "Alisia Fadini", email = "[email protected]" },
-    { name = "Thomas Lane", email = "thomas.lane@desy.de" }
+    { name = "Thomas Lane", email = "thomas.joseph.lane@gmail.com" }
 ]
 requires-python = ">=3.11"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
 dependencies = [
     "numpy >= 1.26",
     "scipy >= 1.14.0",
@@ -24,15 +29,23 @@ dependencies = [
 tests = [
     "pytest",
     "pytest-cov",
+    "pytest-xdist",
 ]
 
 [project.scripts]
 "meteor.diffmap" = "meteor.scripts.compute_difference_map:main"
 "meteor.phaseboost" = "meteor.scripts.compute_iterative_tv_map:main"
 
+[project.urls]
+Homepage = "https://github.com/rs-station/meteor"
+Issues = "https://github.com/rs-station/meteor/issues"
+
 [tool.setuptools_scm]
 version_file = "meteor/_version.py"
 
+[tool.pytest.ini_options]
+addopts = "-n 4 --cov=meteor --cov-report=xml"
+
 [tool.mypy]
 disallow_untyped_calls = true
 disallow_untyped_defs = true
@@ -101,6 +114,3 @@ exclude = [
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
-
-[tool.pytest.ini_options]
-addopts = "--cov=meteor --cov-report=xml"

test/functional/test_compute_difference_map.py

@@ -4,12 +4,17 @@
 import pytest
 import reciprocalspaceship as rs
 
+from meteor import settings
 from meteor.rsmap import Map
 from meteor.scripts import compute_difference_map
 from meteor.scripts.common import WeightMode
 from meteor.tv import TvDenoiseResult
 from meteor.utils import filter_common_indices
 
+# faster tests
+settings.MAP_SAMPLING = 1
+settings.TV_MAX_NUM_ITER = 10
+
 
 @pytest.mark.parametrize("kweight_mode", list(WeightMode))
 @pytest.mark.parametrize("tv_weight_mode", list(WeightMode))

test/functional/test_compute_iterative_tv_map.py

@@ -3,11 +3,16 @@
 import numpy as np
 import reciprocalspaceship as rs
 
+from meteor import settings
 from meteor.rsmap import Map
 from meteor.scripts import compute_iterative_tv_map
 from meteor.scripts.common import read_combined_metadata
 from meteor.utils import filter_common_indices
 
+# faster tests
+settings.MAP_SAMPLING = 1
+settings.TV_MAX_NUM_ITER = 10
+
 
 def test_script_produces_consistent_results(
     testing_pdb_file: Path,

test/unit/test_rsmap.py

@@ -345,6 +345,7 @@ def test_ccp4_map_round_trip(
     assert_phases_allclose(
         random_difference_map.phases.to_numpy(),
         output_coefficients.phases.to_numpy(),
+        atol=0.01,
     )
 
 

test/unit/test_scale.py

@@ -132,5 +132,5 @@ def test_scale_maps_uncertainty_weighting() -> None:
         weight_using_uncertainties=True,
     )
 
-    np.testing.assert_allclose(scaled["F"][(0, 0, 2)], 0.5)
-    np.testing.assert_allclose(scaled["SIGF"][(0, 0, 2)], 250000.0)
+    np.testing.assert_allclose(scaled["F"][(0, 0, 2)], 0.5, atol=1e-4)
+    np.testing.assert_allclose(scaled["SIGF"][(0, 0, 2)], 250000.0, rtol=1e-4)