Merge pull request #5 from ilastik/add-auto-deploy

add automatic deploy via ci

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/deploy.yml

@@ -0,0 +1,34 @@
+name: deploy
+
+on:
+  push:
+    tags:
+      - '1.*'
+
+jobs:
+  package:
+    strategy:
+    runs-on: ubuntu-latest
+    env:
+      ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: install xvfb/deps
+        run: |
+          sudo apt-get update
+          sudo apt-get install -yy mesa-utils libgl1-mesa-dev xvfb curl
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: bld-env
+          environment-file: .github/workflows/etc/bld-environment.yml
+          condarc-file: .github/workflows/etc/conda-rc-deploy.yml
+          miniforge-variant: Miniforge3
+          use-mamba: true
+      - name: linux conda build
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: xvfb-run --server-args="-screen 0 1024x768x24" conda mambabuild -c conda-forge conda-recipe

.github/workflows/etc/bld-environment.yml

@@ -0,0 +1,9 @@
+name: bld-env
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - anaconda-client
+  - conda-build
+  - setuptools_scm
+  - boa

.github/workflows/etc/conda-rc-deploy.yml

@@ -0,0 +1 @@
+anaconda_upload: True

.github/workflows/test.yaml → .github/workflows/test.yml

@@ -18,15 +18,16 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -yy mesa-utils libgl1-mesa-dev xvfb curl
-      - name: setup conda
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           auto-activate-base: true
-          activate-environment: ""
+          activate-environment: bld-env
+          environment-file: .github/workflows/etc/bld-environment.yml
+          miniforge-variant: Miniforge3
+          use-mamba: true
       - name: linux conda build test
         shell: bash -l {0}
         run: |
-          conda install -n base -c conda-forge mamba boa -y
           xvfb-run --server-args="-screen 0 1024x768x24" conda mambabuild --override-channels \
           -c conda-forge conda-recipe

.gitignore

@@ -13,3 +13,5 @@ ilastikrag.egg-info
 *.jpg
 *.swp
 *.ipynb_checkpoints
+
+ilastikrag/_version.py

conda-recipe/meta.yaml

@@ -1,26 +1,25 @@
+{% set setup_py_data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %}
+
 package:
     name: ilastikrag
-
-  {% if GIT_DESCRIBE_NUMBER|int == 0 %}
-    version: {{GIT_DESCRIBE_TAG}}
-  {% else %}
-    # If we're using a non-tagged revision, append '.postN' to the version
-    version: {{GIT_DESCRIBE_TAG}}.post{{GIT_DESCRIBE_NUMBER}}
-  {% endif %}
+    version: {{ setup_py_data.version }}
 
 source:
   path: ../
 
 build:
   noarch: python
   number: 0
-  string: py_{{PKG_BUILDNUM}}_g{{GIT_FULL_HASH[:7]}}
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{ setup_py_data.version }}
   script: python -m pip install --no-deps --ignore-installed .
 
 requirements:
-  build:
+  host:
     - python >=3.7
     - pip
+    - setuptools >=40.0
+    - setuptools_scm
   run:
     - python >=3.7
     # vigra/numpy incompatibility - related to indexing with a non-tuple sequence

dev/README.md

@@ -3,7 +3,8 @@
 ## Create a development environment
 
 ```bash
-conda env create --file dev/environment-dev.py
+conda env create --file dev/environment-dev.yaml --name irag-dev
+conda run --name irag-dev pip install -e .
 ```
 
-This will create an environment with the name `ilastikrag-dev`, that can be activated with `conda activate ilastikrag-dev`.
+This will create an environment with the name `irag-dev`, that can be activated with `conda activate irag-dev`.

dev/environment-dev.yaml

@@ -1,11 +1,12 @@
-name: ilastikrag-dev
 channels:
   - conda-forge
 dependencies:
   - h5py
   - networkx
   - numpy>=1.12,<1.20
   - pandas
+  - pip
   - pytest
   - python>=3.7
+  - setuptools_scm
   - vigra

ilastikrag/__init__.py

@@ -1,6 +1,19 @@
-from __future__ import absolute_import
-from .version import __version__
 from . import accumulators
 from .accumulators import BaseEdgeAccumulator
 from .accumulators import BaseSpAccumulator
 from .rag import Rag
+
+try:
+    from ._version import version
+except ModuleNotFoundError:
+    raise RuntimeError(
+        "Couldn't determine ilastik version - if you are developing ilastik please "
+        "make sure to use an editable install (`pip install -e .`). "
+        "Otherwise, please report this issue to the ilastik development team: team@ilastik.org"
+    )
+
+##################
+# # Version info ##
+##################
+
+__version__ = version

setup.py

@@ -1,54 +1,17 @@
 #!/usr/bin/env python
 
-import os
-import subprocess
 from setuptools import setup, find_packages
+import setuptools_scm
 
-def determine_version(default_version_file):
-    # If running in conda-build, read version from the environment.
-    if 'PKG_VERSION' in os.environ:
-        auto_version = os.environ['PKG_VERSION']
-    else:
-        # Try getting it from the latest git tag
-        try:
-            commit_details = subprocess.check_output("git describe --tags --long HEAD".split()).decode('utf-8')
-            last_tag, commits_since_tag = commit_details.split('-')[:2]
-            auto_version = last_tag
-            if int(commits_since_tag) > 0:
-                # Append commit count to version
-                # (BTW, the .post## convention is recognized by PEP440)
-                # For example: '0.2.post5'
-                auto_version = last_tag + '.post' + commits_since_tag
-        except subprocess.CalledProcessError:
-            # Weird: We're not in a git repo or conda-bld/work.
-            # Read the default value from the source code, I guess.
-            version_globals = {}
-            exec(compile(open(default_version_file).read(), default_version_file, 'exec'), version_globals)
-            auto_version = version_globals['__version__']
-    return auto_version
+_version = setuptools_scm.get_version(write_to="ilastikrag/_version.py")
 
-VERSION_FILE = 'ilastikrag/version.py'
-auto_version = determine_version(VERSION_FILE)
-
-# Cache version.py, then overwrite it with the auto-version
-with open(VERSION_FILE, 'r') as f:
-    orig_version_contents = f.read()
-
-with open(VERSION_FILE, 'w') as f:
-    f.write("__version__ = '{}'\n".format(auto_version))
-
-try:
-    setup(name='ilastikrag',
-          version=auto_version,
-          description='ND Region Adjacency Graph with edge feature algorithms',
-          author='Stuart Berg',
-          author_email='bergs@janelia.hhmi.org',
-          url='github.com/stuarteberg/ilastikrag',
-          packages=find_packages()
-          ## see conda-recipe/meta.yaml for dependency information
-          ##install_requires=['numpy', 'h5py', 'pandas', 'vigra', 'networkx']
-         )
-finally:
-    # Restore the version.py source as it was
-    with open(VERSION_FILE, 'w') as f:
-        f.write(orig_version_contents)
+setup(name='ilastikrag',
+      version=_version,
+      description='ND Region Adjacency Graph with edge feature algorithms',
+      author='Stuart Berg',
+      author_email='bergs@janelia.hhmi.org',
+      url='github.com/stuarteberg/ilastikrag',
+      packages=find_packages()
+      ## see conda-recipe/meta.yaml for dependency information
+      ##install_requires=['numpy', 'h5py', 'pandas', 'vigra', 'networkx']
+)