Merge pull request #154 from kabilar/main

Update GitHub Actions, Dev Container, and dependencies

Author: Thinh Nguyen

.devcontainer/Dockerfile

@@ -30,17 +30,11 @@ RUN \
 COPY ./ /tmp/element-calcium-imaging/
 
 RUN \
-    # workflow dependencies
-    # apt-get install gcc ffmpeg libsm6 libxext6 -y && \
-    # pip install --no-cache-dir Pygments==2.14.0  && \
-    # git clone https://github.com/datajoint/CaImAn.git  && \
-    # pip install --no-cache-dir -r ./CaImAn/requirements.txt  && \
-    # pip install --no-cache-dir ./CaImAn && \
-    pip install git+https://github.com/datajoint/sbxreader && \
-    pip install git+https://github.com/atlab/scanreader && \
-    pip install --no-cache-dir -e /tmp/element-calcium-imaging[elements,nd2,suite2p,tests] && \
+    # pipeline dependencies
+    apt-get install gcc g++ ffmpeg libsm6 libxext6 -y && \
+    pip install --no-cache-dir -e /tmp/element-calcium-imaging[caiman_requirements] && \
+    pip install --no-cache-dir -e /tmp/element-calcium-imaging[caiman,elements,nd2,sbxreader,scanreader,suite2p,tests] && \
     # clean up
-    # rm -rf /tmp/CaImAn && \
     rm -rf /tmp/element-calcium-imaging && \
     apt-get clean
 

.devcontainer/devcontainer.json

@@ -23,7 +23,7 @@
 		"vscode": {
 			"extensions": [
 				"[email protected]",
-				"[email protected]",
+				"[email protected]"
 			]
 		}
 	}

.devcontainer/docker-compose.yaml

@@ -4,9 +4,9 @@ services:
     cpus: 4
     mem_limit: 8g
     # build:
-    #   context: ../..
+    #   context: ..
     #   dockerfile: ./.devcontainer/Dockerfile
-    image: datajoint/element_calcium_imaging_devcontainer:latest
+    image: datajoint/element_calcium_imaging:latest
     extra_hosts:
       - fakeservices.datajoint.io:127.0.0.1
     environment:

.github/workflows/test.yaml

@@ -3,6 +3,8 @@ on:
   push:
   pull_request:
   workflow_dispatch:
+  schedule:
+    - cron: "0 8 * * 1"
 jobs:
   devcontainer-build:
     uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main

CHANGELOG.md

@@ -3,7 +3,14 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.7.8] - 2023-07-23
+## [0.7.9] - 2023-07-27
+
++ Update - GitHub Actions to run every Monday at 8am
++ Update - Dev Container to install CaImAn and rename Docker image
++ Update - `extras_require` to increment `element-interface` version
++ Update - `extras_require` to include `caiman`, `sbxreader`, and `scanreader`
+
+## [0.7.8] - 2023-07-27
 
 + Update - import statement for `prairie_view_loader` in `scan.py`
 
@@ -160,6 +167,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `scan` and `imaging` modules
 + Add - Readers for `ScanImage`, `ScanBox`, `Suite2p`, `CaImAn`
 
+[0.7.9]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.9
 [0.7.8]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.8
 [0.7.7]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.7
 [0.7.6]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.6

Dockerfile

@@ -21,7 +21,9 @@ combined with other Elements to assemble a fully functional pipeline.
 
 ![pipeline](https://raw.githubusercontent.com/datajoint/element-calcium-imaging/main/images/pipeline_imaging.svg)
 
-+ We have designed three variations of the pipeline to handle different use cases. Displayed above is the default `imaging` schema.  Details on all of the `imaging` schemas can be found in the [Data Pipeline](./pipeline.md) documentation page.
++ We have designed three variations of the pipeline to handle different use cases. 
+Displayed above is the default `imaging` schema.  Details on all of the `imaging` 
+schemas can be found in the [Data Pipeline](./pipeline.md) documentation page.
 
 ## Getting Started
 
@@ -39,4 +41,5 @@ combined with other Elements to assemble a fully functional pipeline.
 
 ## Support
 
-+ If you need help getting started or run into any errors, please contact our team by email at [email protected].
++ If you need help getting started or run into any errors, please contact our team by 
+email at [email protected].

docker-compose-build.yaml

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from os import path
-
 from setuptools import find_packages, setup
+import urllib.request
 
 pkg_name = "element_calcium_imaging"
 here = path.abspath(path.dirname(__file__))
@@ -12,6 +12,14 @@
 with open(path.join(here, pkg_name, "version.py")) as f:
     exec(f.read())
 
+with urllib.request.urlopen(
+    "https://raw.githubusercontent.com/flatironinstitute/CaImAn/master/requirements.txt"
+) as f:
+    caiman_requirements = f.read().decode("UTF-8").split("\n")
+
+caiman_requirements.remove("")
+caiman_requirements.append("future")
+
 setup(
     name=pkg_name.replace("_", "-"),
     version=__version__,  # noqa: F821
@@ -32,15 +40,19 @@
         "plotly",
     ],
     extras_require={
+        "caiman_requirements": [caiman_requirements],
+        "caiman": ["caiman @ git+https://github.com/datajoint/CaImAn"],
         "elements": [
             "element-animal>=0.1.8",
             "element-event>=0.2.3",
-            "element-interface>=0.5.4",
+            "element-interface>=0.6.0",
             "element-lab>=0.3.0",
             "element-session>=0.1.5",
         ],
         "extract": ["matlabengine", "scipy"],
         "nd2": ["nd2"],
+        "sbxreader": ["sbxreader @ git+https://github.com/jcouto/sbxreader"],
+        "scanreader": ["scanreader @ git+https://github.com/atlab/scanreader"],
         "suite2p": ["suite2p[io]>=0.12.1"],
         "tests": ["pytest", "pytest-cov", "shutils"],
     },