Merge pull request #110 from nel-lab/organize-for-release

organizing stuff for release

.github/workflows/python-package-conda.yml → .github/workflows/linux-conda.yml

@@ -9,7 +9,7 @@ on:
     branches: [ master ]
 
 jobs:
-  build-linux:
+  build-linux-conda:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
@@ -38,10 +38,9 @@ jobs:
       run: |
         mamba env update -n base --file environment.yml
         caimanmanager.py install
-        pip install "pandas==1.5.0rc0"
         pip install .
         
     - name: Test with pytest
       run: |
-        mamba install pytest
         DOWNLOAD_GROUND_TRUTHS=1 pytest -s .
+

.github/workflows/python-app.yml → .github/workflows/linux-pip.yml

@@ -15,7 +15,7 @@ permissions:
   contents: read
 
 jobs:
-  build:
+  build-linux-pip:
 
     runs-on: ubuntu-latest
 
@@ -41,8 +41,6 @@ jobs:
 
     - name: Install mesmerize-core
       run: |
-        pip install -r requirements.txt
-        pip install pytest
         pip install .        
         
     - name: Test with pytest

.github/workflows/macos-conda.yml

@@ -0,0 +1,46 @@
+name: MacOS Conda
+
+on:
+  pull_request:
+    branches:
+      - master
+      - dev
+  push:
+    branches: [ master ]
+
+jobs:
+  build-macos-conda:
+    runs-on: macos-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python '3.10'
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+        
+    - name: Install mamba
+      run: |
+        conda install -c conda-forge mamba
+        conda clean -a
+        
+        #   - name: install caiman
+        #     run: |
+        #       mamba install -c conda-forge caiman
+        
+    - name: install mesmerize-core
+      run: |
+        mamba env update -n base --file environment.yml
+        caimanmanager.py install
+        pip install .
+        
+    - name: Test with pytest
+      run: |
+        DOWNLOAD_GROUND_TRUTHS=1 pytest -s .
+

.github/workflows/conda-windows.yml → .github/workflows/windows-conda.yml

@@ -9,7 +9,7 @@ on:
     branches: [ master ]
 
 jobs:
-  build:
+  build-windows:
     name: windows conda
     runs-on: "windows-latest"
     steps:
@@ -35,6 +35,5 @@ jobs:
           conda activate mescore
           mamba install pytest
           caimanmanager.py install
-          pip install "pandas==1.5.0rc0"
           pip install .
           DOWNLOAD_GROUND_TRUTHS=1 pytest -s .

MANIFEST.in

@@ -0,0 +1,2 @@
+include mesmerize_core/VERSION
+

environment.yml

@@ -2,7 +2,13 @@ channels:
   - conda-forge
 dependencies:
   - caiman >= 1.9.10
-  - pandas
+  - pandas >= 1.5.0
   - requests
   - click
+  - jupyterlab
+  - tqdm
+  - pims
+  - psutil
+  - pytest
   - pydata-sphinx-theme
+

mesmerize_core/VERSION

@@ -0,0 +1 @@
+0.1.0b1

mesmerize_core/__init__.py

@@ -5,6 +5,11 @@
     create_batch,
 )
 from .caiman_extensions import *
+from pathlib import Path
+
+
+with open(Path(__file__).parent.joinpath("VERSION"), "r") as f:
+    __version__ = f.read().split("\n")[0]
 
 __all__ = [
     "set_parent_raw_data_path",

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+

setup.py

@@ -1,12 +1,53 @@
 from setuptools import setup, find_packages
+from pathlib import Path
+
+
+install_requires = [
+    "pandas>=1.5.0",
+    "pytest",
+    "requests",
+    "tqdm",
+    "numpy",
+    "matplotlib",
+    "click",
+    "psutil",
+    "pims",
+    "jupyterlab",
+]
+
+
+with open(Path(__file__).parent.joinpath("README.md")) as f:
+    readme = f.read()
+
+with open(Path(__file__).parent.joinpath("mesmerize_core", "VERSION"), "r") as f:
+    ver = f.read().split("\n")[0]
+
+
+classifiers = \
+    [
+        "Programming Language :: Python :: 3",
+        "LICENSE :: OSI APPROVED :: APACHE SOFTWARE LICENSE",
+        "Operating System :: POSIX :: Linux",
+        "Operating System :: MacOS :: MacOS X",
+        "Operating System :: Microsoft :: Windows :: Windows 10",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Image Recognition",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+        "Intended Audience :: Science/Research"
+    ]
+
 
 setup(
     name="mesmerize-core",
-    version="0.0",
+    description="High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn",
+    long_description=readme,
+    classifiers=classifiers,
+    version=ver,
+    install_requires=install_requires,
     packages=find_packages(),
+    include_package_data=True,
     url="https://github.com/nel-lab/mesmerize-core",
-    license="Apache",
-    author="Kushal Kolar, Arjun Putcha",
+    license="Apache-Software-License",
+    author="Kushal Kolar, Caitlin Lewis, Arjun Putcha",
     author_email="",
-    description="Mesmerize core backend",
 )