Merge pull request #38 from scalableminds/matrix_tests

Add matrix tests to GitHub Actions CI

.github/workflows/publish.yml

@@ -0,0 +1,28 @@
+name: Build and Upload Python Package
+
+on: 
+  release:
+    types:
+      - created
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.7'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install poetry
+        poetry install
+ 
+    - name: Build and publish
+      env:
+        PYPI_SCM_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        PYPI_SCM_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        poetry publish --build -u $PYPI_SCM_USERNAME -p $PYPI_SCM_PASSWORD

.github/workflows/python-module.yml → .github/workflows/test.yml

@@ -1,36 +1,39 @@
-name: Test and Upload Python Package
+name: Test Python Package
 
 on: [push]
 
 jobs:
-  deploy:
+  test:
     runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
       uses: actions/setup-python@v1
       with:
-        python-version: '3.6'
+        python-version: ${{ matrix.python-version }}
+        architecture: 'x64' # (x64 or x86)
+
     - name: Install dependencies
       run: |
         python -m pip install poetry
         poetry install
+
     - name: Check formatting
       run: |
         poetry run black --check wknml tests examples
+
     - name: Unit Tests
       run: |
         mkdir -p testoutput
         poetry run pytest tests
+
     - name: Check Documentation for updates
       run: |
         poetry run pydoc-markdown -m wknml --render-toc > docs/ci_test.md
         diff docs/ci_test.md docs/wknml.md
         rm docs/ci_test.md
-    - name: Build and publish
-      if: startsWith(github.event.ref, 'refs/tags')
-      env:
-        PYPI_SCM_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        PYPI_SCM_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        poetry publish --build -u $PYPI_SCM_USERNAME -p $PYPI_SCM_PASSWORD

README.md

@@ -1,13 +1,14 @@
 # wknml
 [![PyPI version](https://img.shields.io/pypi/v/wknml)](https://pypi.python.org/pypi/wknml)
 [![Supported Python Versions](https://img.shields.io/pypi/pyversions/wknml.svg)](https://pypi.python.org/pypi/wknml)
+[![Build Status](https://img.shields.io/github/workflow/status/scalableminds/wknml/Test%20Python%20Package/master)](https://github.com/scalableminds/wknml/actions?query=workflow%3A%22Test+Python+Package%22)
 [![Documentation](https://img.shields.io/badge/docs-passing-brightgreen.svg)](https://github.com/scalableminds/wknml/blob/master/docs/wknml.md)
+[![Code Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-
-Python library for working with [webKnossos](https://webknossos.org) [NML files](https://docs.webknossos.org/reference/data_formats#nml).
+Python library for working with [webKnossos](https://webknossos.org) [skeleton annotation files (NML)](https://docs.webknossos.org/reference/data_formats#nml).
 
 ## Installation
-To use wknml, you need to have Python 3.6+ (on the system or with Anaconda) installed.
+wknml requires Python 3.6+
 
 ```
 pip install wknml

pyproject.toml

@@ -1,8 +1,10 @@
 [tool.poetry]
 name = "wknml"
-version = "1.0.0"
+version = "1.0.1"
 description = "Python package to work with webKnossos NML skeleton files"
 authors = ["scalable minds <[email protected]>"]
+readme = "README.md"
+repository = "https://github.com/scalableminds/wknml"
 license = "MIT"
 
 [tool.poetry.dependencies]

tests/refresh_snapshots.py

@@ -1,17 +1,7 @@
 import wknml
-import pickle
 from tests.test_snapshot_readandwrite import INPUT_FILES, OUTPUT_FILES, SNAPSHOT_FILES
 
 
-def save_snapshot_pickle_read_and_write():
-    for i in range(0, len(INPUT_FILES)):
-        input_file = INPUT_FILES[i]
-        output_file = SNAPSHOT_FILES[i]
-        parsed = wknml.parse_nml(input_file)
-        with open(output_file + ".pickle", "wb") as f:
-            pickle.dump(parsed, f)
-
-
 def save_snapshot_nml_read_and_write():
     for i in range(0, len(INPUT_FILES)):
         input_file = INPUT_FILES[i]
@@ -22,5 +12,4 @@ def save_snapshot_nml_read_and_write():
 
 
 if __name__ == "__main__":
-    save_snapshot_pickle_read_and_write()
     save_snapshot_nml_read_and_write()

tests/test_nml_generation.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+import pickle
 
 import pytest
 import filecmp
@@ -36,23 +37,40 @@ def test_generate_nml():
 def test_no_default_values_written():
     input_file_name = "testdata/nml_without_default_values.nml"
     output_file_name = "testoutput/nml_without_default_values.nml"
+
     # read and write the test file
     with open(input_file_name, "r") as file:
         test_nml = parse_nml(file)
-        with open(output_file_name, "wb") as output_file:
-            write_nml(file=output_file, nml=test_nml)
+
+    with open(output_file_name, "wb") as output_file:
+        write_nml(file=output_file, nml=test_nml)
 
     # read the written testfile and compare the content
-    with open(input_file_name, "r") as file:
-        test_nml = parse_nml(file)
-        with open(output_file_name, "r") as output_file:
-            test_result_nml = parse_nml(output_file)
+    with open(output_file_name, "r") as output_file:
+        test_result_nml = parse_nml(output_file)
 
-            assert (
-                test_nml == test_result_nml
-            ), "The testdata file and the testoutput file do not have the same content."
+    assert (
+        test_nml == test_result_nml
+    ), "The testdata file and the testoutput file do not have the same content."
 
     # test if both files have the same content
     assert filecmp.cmp(
         input_file_name, output_file_name
     ), "The testdata and the testoutput file do not have the same content."
+
+
+def test_pickle_serialization():
+    # Test if NML objects can be serialized & deserialized with pickle
+    input_file_name = "testdata/nml_without_default_values.nml"
+    output_file_name = "testoutput/nml_without_default_values.nml.pickle"
+
+    with open(input_file_name, "r") as file:
+        test_nml = parse_nml(file)
+
+    with open(output_file_name, "wb") as output_file:
+        pickle.dump(test_nml, output_file)
+
+    with open(output_file_name, "rb") as input_file:
+        new_nml = pickle.load(input_file)
+
+    assert test_nml == new_nml

tests/test_snapshot_readandwrite.py

@@ -20,30 +20,25 @@ def test_read_and_write_and_read():
     for i in range(0, len(INPUT_FILES)):
         input_file = INPUT_FILES[i]
         output_file = OUTPUT_FILES[i]
+
         first = wknml.parse_nml(input_file)
+
         with open(output_file, "wb") as f:
             wknml.write_nml(f, first)
+
         second = wknml.parse_nml(output_file)
         assert first == second
 
 
-def test_snapshot_read_and_compare_pickle():
-    for i in range(0, len(INPUT_FILES)):
-        input_file = INPUT_FILES[i]
-        snapshot_file = SNAPSHOT_FILES[i]
-        output_file = OUTPUT_FILES[i]
-        parsed = wknml.parse_nml(input_file)
-        with open(output_file + ".pickle.cmp", "wb") as f:
-            pickle.dump(parsed, f)
-        assert filecmp.cmp(snapshot_file + ".pickle", output_file + ".pickle.cmp")
-
-
 def test_snapshot_read_and_compare_nml():
     for i in range(0, len(INPUT_FILES)):
         input_file = INPUT_FILES[i]
         snapshot_file = SNAPSHOT_FILES[i]
         output_file = OUTPUT_FILES[i]
+
         parsed = wknml.parse_nml(input_file)
+
         with open(output_file, "wb") as f:
             wknml.write_nml(f, parsed)
+
         assert filecmp.cmp(snapshot_file + ".snapshot", output_file)