Move to setup.cfg based install (#61)

* Move from poetry to standard setup.cfg based install
* Fix actions
* Fix requirements
* Add flake8 as dev dependency
* Update pre-commit versions
* Fix test

.github/workflows/publish.yml

@@ -9,19 +9,19 @@ jobs:
     runs-on: windows-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v1
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       with:
-        python-version: 3.7
-        architecture: x64
+        python-version: 3.9
 
-    - name: Install with poetry
+    - name: Install dependencies
       run: |
-        pip install poetry
-
-    - name: Build with poetry
-      run: poetry build
-
-    - name: Publish with poetry
-      run: |
-        poetry publish -u ${{ secrets.pypi_user }} -p ${{ secrets.pypi_pw }}
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+        python setup.py sdist bdist_wheel
+    
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test.yml

@@ -1,10 +1,18 @@
 name: build
 
 on:
-  push:
-    branches: [ master ]
   pull_request:
-    branches: [ master ]
+    branches:
+      - main
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+  push:
+    branches:
+      - main
+  workflow_dispatch:
 
 jobs:
   build:
@@ -16,30 +24,29 @@ jobs:
         python-version: [3.7, 3.8, 3.9]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
 
+    - uses: actions/cache@v3
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}
+
+    - name: Install
+      run: |
+        python -m pip install -e .[develop]
+
     - name: Lint with flake8
       run: |
-        pip install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore E501
 
-    - name: Install with poetry
-      run: |
-        pip install poetry
-        # poetry install --no-dev
-        poetry install
-
     - name: Test with pytest
       run: |
-        poetry run pytest tests
-
-    - name: Build with poetry
-      run: poetry build
+        pytest tests

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
@@ -17,26 +17,26 @@ repos:
     # -   id: check-json
     # -   id: check-added-large-files
 -   repo: https://github.com/myint/docformatter
-    rev: v1.4
+    rev: v1.5.0
     hooks:
     -   id: docformatter
 -   repo: https://github.com/asottile/reorder_python_imports
-    rev: v2.5.0
+    rev: v3.9.0
     hooks:
     -   id: reorder-python-imports
         args: [--py3-plus]
 -   repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v1.5.7
+    rev: v2.0.1
     hooks:
     -   id: autopep8
         args: ['--in-place', '--ignore=E501,W504']
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.15.0
+    rev: v3.3.1
     hooks:
     -   id: pyupgrade
         args: ['--py36-plus']
-  - repo: https://github.com/PyCQA/flake8
-    rev: '5.0.4'
+-   repo: https://github.com/PyCQA/flake8
+    rev: '6.0.0'
     hooks:
     -   id: flake8
         args: ['--statistics', '--ignore=F401,F403,F405,F821,F841,E265,E501,A003']
@@ -51,8 +51,8 @@ repos:
           'flake8-type-annotations',
           'flake8-builtins',
           ]
-- repo: https://github.com/kynan/nbstripout
-  rev: 0.4.0
-  hooks:
-    - id: nbstripout
-      files: ".ipynb"
+-   repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+    -   id: nbstripout
+        files: ".ipynb"

MANIFEST.in

@@ -0,0 +1,29 @@
+include .pre-commit-config.yaml
+include THANKS.md
+include LICENCE
+include notebooks/*.ipynb
+include notebooks/nav.nav
+include notebooks/readme.md
+include docs/*.md
+include docs/*.png
+include docs/*.py
+include requirements.txt
+include scripts/*.py
+include setup_win.bat
+include tests/*.py
+include tests/config/*.yaml
+include tests/config/*/*.yaml
+include instamatic/camera/*.dll
+include instamatic/camera/*.h
+include instamatic/camera/*.lockfile
+include instamatic/camera/*.md
+include instamatic/camera/tpx/*.bpc
+include instamatic/camera/tpx/*.dacs
+include instamatic/camera/tpx/*.txt
+include instamatic/config/*.yaml
+include instamatic/config/alignments/*.yaml
+include instamatic/config/calibration/*.yaml
+include instamatic/config/camera/*.yaml
+include instamatic/config/microscope/*.yaml
+include instamatic/config/scripts/*.md
+include instamatic.neural_network/*.p