Merge branch 'main' into codyheiser/main

.bumpversion.cfg

@@ -0,0 +1,8 @@
+[bumpversion]
+current_version = 0.0.1
+tag = True
+commit = False
+
+[bumpversion:file:./pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"

.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+    require_ci_to_pass: no
+
+coverage:
+    status:
+        project:
+            default:
+                # Require 1% coverage, i.e., always succeed
+                target: 1
+        patch: false
+        changes: false
+
+comment:
+    layout: diff, flags, files
+    behavior: once
+    require_base: no

.cruft.json

@@ -0,0 +1,19 @@
+{
+    "template": "https://github.com/scverse/cookiecutter-scverse",
+    "commit": "f5efdc5d14da023ef86a932b6bc583c7b243d2c9",
+    "context": {
+        "cookiecutter": {
+            "project_name": "infercnvpy",
+            "package_name": "infercnvpy",
+            "project_description": "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. ",
+            "author_full_name": "Gregor Sturm",
+            "author_email": "mail@gregor-sturm.de",
+            "github_user": "grst",
+            "project_repo": "https://github.com/icbi-lab/infercnvpy",
+            "license": "BSD 3-Clause License",
+            "_copy_without_render": [".github/workflows/**.yaml"],
+            "_template": "https://github.com/scverse/cookiecutter-scverse"
+        }
+    },
+    "directory": null
+}

.editorconfig

@@ -1,15 +1,12 @@
 root = true
 
 [*]
-charset = utf-8
+indent_style = space
+indent_size = 4
 end_of_line = lf
-insert_final_newline = true
+charset = utf-8
 trim_trailing_whitespace = true
-max_line_length = 88
-
-[*.py]
-indent_size = 4
-indent_style = space
+insert_final_newline = true
 
 [Makefile]
 indent_style = tab

.flake8

@@ -0,0 +1,56 @@
+# Can't yet be moved to the pyproject.toml due to https://github.com/PyCQA/flake8/issues/234
+[flake8]
+max-line-length = 120
+ignore =
+    # line break before a binary operator -> black does not adhere to PEP8
+    W503
+    # line break occured after a binary operator -> black does not adhere to PEP8
+    W504
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    E501
+    # whitespace before : -> black does not adhere to PEP8
+    E203
+    # missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
+    E231
+    # continuation line over-indented for hanging indent -> black does not adhere to PEP8
+    E126
+    # E266 too many leading '#' for block comment -> this is fine for indicating sections
+    E262
+    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+    E731
+    # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
+    E741
+    # Missing docstring in public package
+    D104
+    # ... imported but unused
+    F401
+    # Missing docstring in public module
+    D100
+    # Missing docstring in __init__
+    D107
+    # Do not perform function calls in argument defaults.
+    B008
+    # line break before binary operator
+    W503
+    # Missing docstring in magic method
+    D105
+    # whitespace before ':'
+    E203
+    # format string does contain unindexed parameters
+    P101
+    # first line should end with a period [Bug: doesn't work with single-line docstrings]
+    D400
+    # First line should be in imperative mood; try rephrasing
+    D401
+    # undefined RST roles
+    RST304
+    # RST definition list ends without a blank linke; unexpected unindent
+    RST203
+    # ignore false positive warnings due to *args, **kwargs
+    RST210
+
+
+exclude = .git,__pycache__,build,docs/_build,dist
+per-file-ignores =
+    tests/*: D
+    */__init__.py: F401

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    package:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v2
+              with:
+                  python-version: "3.10"
+            - name: Install build dependencies
+              run: python -m pip install --upgrade pip wheel twine build
+            - name: Build package
+              run: python -m build
+            - name: Check package
+              run: twine check --strict dist/*.whl

.github/workflows/sync.yaml

@@ -0,0 +1,43 @@
+name: Sync Template
+
+on:
+    workflow_dispatch:
+    schedule:
+        - cron: "0 2 * * *" # every night at 2:00
+
+jobs:
+    sync:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v2
+              with:
+                  python-version: "3.10"
+            - name: Install dependencies
+              run: python -m pip install --upgrade cruft
+            - name: Find Latest Tag
+              uses: oprypin/find-latest-tag@v1.1.0
+              id: get-latest-tag
+              with:
+                  repository: scverse/cookiecutter-scverse
+                  releases-only: false
+                  sort-tags: true
+                  regex: '^v\d+\.\d+\.\d+$' # vX.X.X
+            - name: Sync
+              run: |
+                  cruft update --checkout ${{ steps.get-latest-tag.outputs.tag }} --skip-apply-ask --project-dir .
+            - name: Create Pull Request
+              uses: peter-evans/create-pull-request@v4
+              commit-message: Automated template update from cookiecutter-scverse
+              branch: template-update
+              title: Automated template update from cookiecutter-scverse
+              body: |
+                  A new version of the scverse cookiecutter template got released. This PR
+                  adds all new changes to your repository and helps to to stay in sync with the latest
+                  best-practice template maintained by the scverse team.
+
+                  If a merge conflict arised, a `.rej` file with the rejected patch is generated. You'll need to
+                  manually merge these changes.
+
+                  For more information about the template sync, please refer to the [template documentation](TODO).

.github/workflows/test.yaml

@@ -0,0 +1,77 @@
+name: Test
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        strategy:
+            fail-fast: false
+            matrix:
+                python: ["3.8", "3.10"]
+                os: [ubuntu-latest]
+                r: ["release"]
+
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+            R_KEEP_PKG_SOURCE: yes
+
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v2
+              with:
+                  python-version: ${{ matrix.python }}
+            - uses: r-lib/actions/setup-r@v2
+              with:
+                  r-version: ${{ matrix.r }}
+                  use-public-rspm: true
+
+            - name: Get pip cache dir
+              id: pip-cache-dir
+              run: |
+                  echo "::set-output name=dir::$(pip cache dir)"
+            - name: Restore pip cache
+              uses: actions/cache@v2
+              with:
+                  path: ${{ steps.pip-cache-dir.outputs.dir }}
+                  key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
+                  restore-keys: |
+                      pip-${{ runner.os }}-${{ env.pythonLocation }}-
+            - name: Install test dependencies
+              run: |
+                  python -m pip install --upgrade pip wheel
+                  pip install codecov
+            - name: Install dependencies
+              run: |
+                  pip install ".[dev,test,copykat]"
+
+            - name: Install R dependencies
+              run: |
+                  install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
+                  # TODO: use copykat version from february, latest version seens to have a bug...
+                  pak::pkg_install(c('stringr', 'navinlabcode/copykat@674e331cf12ce14b62eaf6459f7c84a82fc4c775'))
+              shell: Rscript {0}
+
+            - name: Test
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: |
+                  pytest -v --cov --color=yes
+            - name: Upload coverage
+              env:
+                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+              run: |
+                  codecov --required --flags=unittests