dvp-io 0.2.2__tar.gz

dvp_io-0.2.2/.bumpversion.toml

@@ -0,0 +1,40 @@
+[tool.bumpversion]
+current_version = "0.2.2"
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:
+        -                             # dash separator for pre-release section
+        (?P<pre_l>[a-zA-Z-]+)         # pre_l: pre-release label
+        (?P<pre_n>0|[1-9]\\d*)        # pre_n: pre-release version number
+    )?                                # pre-release section is optional
+"""
+serialize = [
+    "{major}.{minor}.{patch}-{pre_l}{pre_n}",
+    "{major}.{minor}.{patch}",
+]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = false
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+[tool.bumpversion.parts.pre_l]
+# 'final' is just a dummy, but required to have the versioning compatible with the reusable alphashared workflow
+values = ["dev", "final"]
+optional_value = "final"
+
+[[tool.bumpversion.files]]
+filename = "./pyproject.toml"

dvp_io-0.2.2/.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

dvp_io-0.2.2/.cruft.json

@@ -0,0 +1,30 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "5d44c58df427f884585ae9772cae81f1b6638f80",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "dvp-io",
+      "package_name": "dvpio",
+      "project_description": "Read and write funtionalities from and to spatialdata for deep vizual proteomics",
+      "author_full_name": "Lucas Diedrich",
+      "author_email": "diedrich@biochem.mpg.de",
+      "github_user": "lucas-diedrich",
+      "github_repo": "dvp-io",
+      "license": "Apache License Version 2.0",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.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
+}

dvp_io-0.2.2/.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

dvp_io-0.2.2/.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

dvp_io-0.2.2/.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.

dvp_io-0.2.2/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for dvp-io
+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

dvp_io-0.2.2/.github/release_notes.yaml

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+# name: Release Notes
+# Automatically generate summary of all channges since last release
+# https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes#configuring-automatically-generated-release-notes
+
+changelog:
+  exclude:
+    labels:
+      - ignore-for-release
+  categories:
+    - title: Breaking Changes
+      labels:
+        - breaking-change
+    - title: Bug fixes
+      labels:
+        - bug
+        - bug-fixes
+    - title: New Features
+      labels:
+        - enhancement
+    - title: Documentation
+      labels:
+        - documentation
+    - title: Other Changes / unlabeled
+      labels:
+        - "*"

dvp_io-0.2.2/.github/workflows/build.yaml

@@ -0,0 +1,32 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          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

dvp_io-0.2.2/.github/workflows/bump_version.yaml

@@ -0,0 +1,23 @@
+# Bump the version for releases
+name: Bump version
+
+on:
+  workflow_dispatch:
+    inputs:
+      bump_type:
+        description: "Bump type"
+        required: true
+        default: "minor"
+        type: choice
+        options:
+          - prerelease
+          - patch
+          - minor
+          - major
+
+jobs:
+  bump-version:
+    uses: MannLabs/alphashared/.github/workflows/bump_version.yml@v1
+    secrets: inherit
+    with:
+      bump_type: ${{ inputs.bump_type }}

dvp_io-0.2.2/.github/workflows/prepare_test_data.yaml

@@ -0,0 +1,46 @@
+name: Prepare test data
+
+on:
+  workflow_dispatch:
+  # Pushing to branch dataset will create a new artifact
+  push:
+    branches:
+      - dataset
+jobs:
+  prepare-data:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Download test datasets
+        run: |
+          set -e
+          rm -rf ./data && mkdir -p ./data
+          curl -o ./data/openslide-mirax.zip https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/Mirax2.2-4-PNG.zip
+          curl -o ./data/zeiss.zip https://datashare.biochem.mpg.de/s/k2C6sg0qrXBdWdc/download
+          curl -o ./data/blobs.zip https://datashare.biochem.mpg.de/s/0oTGB6xpUaWIaVh/download
+          curl -o ./data/triangles.zip https://datashare.biochem.mpg.de/s/zneNg7QxZNM2wSm/download
+          curl -o ./data/omics.zip https://datashare.biochem.mpg.de/s/a9bTNCXBYgE5n5S/download
+
+      - name: Unzip files
+        run: |
+          unzip ./data/openslide-mirax.zip -d ./data/openslide-mirax
+          unzip ./data/zeiss.zip -d ./data/zeiss
+          unzip ./data/blobs.zip -d ./data/blobs
+          unzip ./data/triangles.zip -d ./data
+          unzip ./data/omics.zip -d ./data
+
+      - name: Remove archives
+        run: |
+          rm ./data/openslide-mirax.zip
+          rm ./data/zeiss.zip
+          rm ./data/blobs.zip
+          rm ./data/triangles.zip
+          rm ./data/omics.zip
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: data
+          path: ./data

dvp_io-0.2.2/.github/workflows/release.yaml

@@ -0,0 +1,29 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dvpio
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

dvp_io-0.2.2/.github/workflows/test.yaml

@@ -0,0 +1,83 @@
+name: Test
+
+permissions:
+  actions: read
+  contents: read
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.11"
+          - os: ubuntu-latest
+            python: "3.11"
+            pip-flags: "--pre"
+            name: PRE-RELEASE DEPENDENCIES
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Download artifact of test data
+        uses: dawidd6/action-download-artifact@v6
+        with:
+          workflow: prepare_test_data.yaml
+          name: data
+          path: ./data
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+
+      - name: Install dependencies
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

dvp_io-0.2.2/.gitignore

@@ -0,0 +1,25 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+
+# docs
+/docs/generated/
+/docs/_build/
+/docs/tutorials/mock-data/*
+/docs/tutorials/data/*
+
+
+.coverage

dvp_io-0.2.2/.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.5.0
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.3
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

dvp_io-0.2.2/.prettierrc.yaml

@@ -0,0 +1,7 @@
+overrides:
+  # JSON with comments and trailing commas
+  - files: .vscode/*.json
+    options:
+      parser: json5
+      quoteProps: preserve
+      singleQuote: false

dvp_io-0.2.2/.readthedocs.yaml

@@ -0,0 +1,19 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+  apt_packages:
+    - libssh2-1
+    - libssh2-1.dev
+sphinx:
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: true
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

dvp_io-0.2.2/.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "esbenp.prettier-vscode",
+    ],
+}

dvp_io-0.2.2/.vscode/launch.json

@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}

dvp_io-0.2.2/.vscode/settings.json

@@ -0,0 +1,18 @@
+{
+    "[python][jsonc][yaml]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[jsonc][yaml]": {
+        "editor.defaultFormatter": "esbenp.prettier-vscode",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}

dvp_io-0.2.2/CHANGELOG.md

@@ -0,0 +1,3 @@
+# Changelog
+
+Refer to the [Releases page](https://github.com/lucas-diedrich/dvp-io/releases) for information on releases and the changelog.

dvp_io-0.2.2/CITATION.cff

@@ -0,0 +1,25 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: dvp-io
+message: >-
+    Read and write funtionalities from and to spatialdata for
+    deep visual proteomics
+type: software
+authors:
+    - given-names: Lucas
+      family-names: Diedrich
+      email: diedrich@biochem.mpg.de
+      affiliation: Max-Planck-Institute of Biochemistry
+      name-suffix: †
+      orcid: "https://orcid.org/0009-0007-4884-1422"
+repository-code: "https://github.com/lucas-diedrich/dvp-io"
+url: "https://dvp-io.readthedocs.io/en/latest/index.html"
+abstract: >
+    Read/write functions to and from spatialdata for Deep
+    Visual Proteomics
+keywords:
+    - spatial-omics
+    - proteomics
+license: Apache-2.0