Merge branch 'main' of https://github.com/YosefLab/PopV into cuml_ena…

…bled

.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 +1,28 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "PopV",
+      "package_name": "popv",
+      "project_description": "Consensus prediction of cell type labels with popV",
+      "author_full_name": "Can Ergen",
+      "author_email": "[email protected]",
+      "github_user": "cane11",
+      "project_repo": "https://github.com/YosefLab/PopV.git",
+      "license": "MIT License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
+}

.editorconfig

@@ -1,21 +1,18 @@
-# http://editorconfig.org
-
 root = true
 
 [*]
 indent_style = space
 indent_size = 4
+end_of_line = lf
+charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
-charset = utf-8
-end_of_line = lf
 
-[*.bat]
-indent_style = tab
-end_of_line = crlf
+[*.{yml,yaml}]
+indent_size = 2
 
-[LICENSE]
-insert_final_newline = false
+[.cruft.json]
+indent_size = 2
 
 [Makefile]
 indent_style = tab

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,89 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Version information
+      description: |
+        Please paste below the output of
+
+        ```python
+        import session_info
+        session_info.show(html=False, dependencies=True)
+        ```
+      placeholder: |
+        -----
+        anndata             0.8.0rc2.dev27+ge524389
+        session_info        1.0.0
+        -----
+        asttokens           NA
+        awkward             1.8.0
+        backcall            0.2.0
+        cython_runtime      NA
+        dateutil            2.8.2
+        debugpy             1.6.0
+        decorator           5.1.1
+        entrypoints         0.4
+        executing           0.8.3
+        h5py                3.7.0
+        ipykernel           6.15.0
+        jedi                0.18.1
+        mpl_toolkits        NA
+        natsort             8.1.0
+        numpy               1.22.4
+        packaging           21.3
+        pandas              1.4.2
+        parso               0.8.3
+        pexpect             4.8.0
+        pickleshare         0.7.5
+        pkg_resources       NA
+        prompt_toolkit      3.0.29
+        psutil              5.9.1
+        ptyprocess          0.7.0
+        pure_eval           0.2.2
+        pydev_ipython       NA
+        pydevconsole        NA
+        pydevd              2.8.0
+        pydevd_file_utils   NA
+        pydevd_plugins      NA
+        pydevd_tracing      NA
+        pygments            2.12.0
+        pytz                2022.1
+        scipy               1.8.1
+        setuptools          62.5.0
+        setuptools_scm      NA
+        six                 1.16.0
+        stack_data          0.3.0
+        tornado             6.1
+        traitlets           5.3.0
+        wcwidth             0.2.5
+        zmq                 23.1.0
+        -----
+        IPython             8.4.0
+        jupyter_client      7.3.4
+        jupyter_core        4.10.0
+        -----
+        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+        -----
+        Session information updated at 2022-07-07 17:55

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for PopV
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/workflows/build.yml

@@ -1,25 +1,25 @@
 name: Check Build
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
 
 jobs:
-    package:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v3
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
-            - 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
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - 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/release.yml

@@ -1,32 +1,32 @@
 name: Release
 
 on:
-    push:
-        tags:
-            - "*.*.*"
+  push:
+    tags:
+      - "*.*.*"
 
 jobs:
-    release:
-        name: Release
-        runs-on: ubuntu-latest
-        steps:
-            # will use ref/SHA that triggered it
-            - name: Checkout code
-              uses: actions/checkout@v3
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      # will use ref/SHA that triggered it
+      - name: Checkout code
+        uses: actions/checkout@v3
 
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
 
-            - name: Install hatch
-              run: |
-                  pip install hatch
+      - name: Install hatch
+        run: |
+          pip install hatch
 
-            - name: Build project for distribution
-              run: hatch build
+      - name: Build project for distribution
+        run: hatch build
 
-            - name: Publish a Python distribution to PyPI
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                  password: ${{ secrets.PYPI_TOKEN }}
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}