feat: docstrings and overall design for expectation maximization iterative refinement

.codecov.yml

@@ -0,0 +1,24 @@
+coverage:
+  round: up
+  precision: 2
+  status:
+    patch:
+      default:
+        # basic
+        target: 90%
+        threshold: 2%
+        base: auto
+        flags:
+          - unit
+        # advanced
+        branches:
+          - master
+        if_no_uploads: error
+        if_not_found: error
+        if_ci_failed: error
+        only_pulls: false
+
+# Files to ignore
+ignore:
+  - "data"
+  - "notebooks"

.coveragerc

@@ -0,0 +1,3 @@
+[report]
+fail_under = 90
+show_missing = True

.deepsource.toml

@@ -1,24 +1,18 @@
 version = 1
 
-test_patterns = ["test/**"]
+test_patterns = ["tests/**"]
 
 exclude_patterns = ["README.md"]
 
 [[analyzers]]
 name = "python"
 enabled = true
 
-  [analyzers.meta]
-  runtime_version = "3.x.x"
-
 [[analyzers]]
 name = "test-coverage"
 enabled = true
 
-[[transformers]]
-name = "isort"
-enabled = true
-
 [[transformers]]
 name = "black"
 enabled = true
+

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+docstring-convention = numpy
+import_order_style = smarkets
+max-line-length = 88
+extend-ignore = E203,I202,I100
+exclude = reconstructSPI/__init__.py,reconstructSPI/iterative_refinement/__init.py,tests/__init__.py

.github/auto-assign.yml

@@ -5,10 +5,10 @@ addReviewers: true
 addAssignees: false
 
 # A list of reviewers to be added to pull requests (GitHub user name)
-reviewers: 
+reviewers:
   - fredericpoitevin
 
-# A list of keywords to be skipped the process that add reviewers if pull requests include it 
+# A list of keywords to be skipped the process that add reviewers if pull requests include it
 skipKeywords:
   - wip
 

.github/workflows/lint.yml

@@ -0,0 +1,54 @@
+name: "Lint"
+
+on:
+  push:
+    branches: [master,github-actions-test]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.9]
+        test-folder : ['tests']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+      - name: install dependencies [pip]
+        run:  |
+          pip install --upgrade pip setuptools wheel
+          for req in dev-requirements.txt; do
+            pip install -q -r $req
+          done
+          pip install -e .
+      - name: linting [black and isort]
+        run: |
+          black . --check
+          isort --profile black --check .
+      - name: linting [flake8]
+        run: |
+          flake8 reconstructSPI tests

.github/workflows/test.yml

@@ -0,0 +1,62 @@
+name: "Test"
+
+on:
+  push:
+    branches: [master,github-actions-test]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.7,3.8,3.9]
+        test-folder : ['tests']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+
+      - name: cache conda
+        uses: actions/cache@v1
+        with:
+          path: $CONDA
+          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-conda-
+      - name: install dependencies [conda]
+        run:  |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          $CONDA/bin/conda env update --file environment.yml --name base
+          $CONDA/bin/pip install -e .
+      - name: unit testing [pytest]
+        env:
+          TEST_TOKEN: ${{ secrets.TEST_TOKEN }}
+        run: |
+          $CONDA/bin/pytest --cov-report term --cov-report xml:coverage.xml --cov=reconstructSPI ${{matrix.test-folder}}
+      - name: uploading code coverage [codecov]
+        if: ${{matrix.python-version == 3.7}}
+        run: |
+          bash <(curl -s https://codecov.io/bash) -c

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+default_language_version :
+  python : python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.1.0
+    hooks:
+      - id: check-byte-order-marker
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: mixed-line-ending
+        args:
+          - --fix=no
+      - id: no-commit-to-branch
+        args:
+          - --branch=master
+      - id: check-added-large-files
+        args:
+          - --maxkb=2048
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 21.8b0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.9.3
+    hooks:
+      - id : isort
+        args : ["--profile", "black", "--filter-files"]
+  - repo: https://github.com/asottile/blacken-docs
+    rev: v1.8.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies: [black==20.8b0]
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+    - id: flake8
+      additional_dependencies:
+        - flake8-docstrings
+        - flake8-import-order
+      exclude: reconstructSPI/__init__.py,tests/__init__.py

dev-requirements.txt

@@ -0,0 +1,5 @@
+black
+flake8
+flake8-docstrings
+isort
+pre-commit

environment.yml

@@ -0,0 +1,18 @@
+name: reconstructSPI
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - codecov
+  - coverage
+  - gemmi
+  - numpy
+  - numba
+  - pillow>=8.2.0
+  - pip
+  - pytest
+  - pytest-cov
+  - pytorch
+  - pip :
+      - git+https://github.com/compSPI/simSPI.git
+

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+testpaths = tests
+python_files = *.py
+python_functions = test_*

reconstructSPI/__init__.py

@@ -0,0 +1 @@
+"""Various particle reconstruction methods."""

reconstructSPI/iterative_refinement/__init__.py

@@ -0,0 +1 @@
+"""Iterative refinement reconstruction methods."""