Merge pull request #121 from kushalbakshi/staging

Add `memoized_result` + update calcium imaging utility functions

.github/workflows/mkdocs-release-caller.yml

@@ -0,0 +1,9 @@
+name: mkdocs-release
+on:
+  workflow_dispatch:
+
+jobs:
+  mkdocs_release:
+    uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
+    permissions: 
+      contents: write

.github/workflows/release.yaml

@@ -0,0 +1,10 @@
+name: Release
+on:
+  workflow_dispatch:
+jobs:
+  make_github_release:
+    uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
+  mkdocs_release:
+    uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
+    permissions: 
+      contents: write

.github/workflows/semantic-release-caller.yml

@@ -0,0 +1,7 @@
+name: semantic-release
+on:
+  workflow_dispatch:
+
+jobs:
+  call_semantic_release:
+    uses: datajoint/.github/.github/workflows/semantic-release.yaml@main

.github/workflows/test.yaml

@@ -0,0 +1,35 @@
+name: Test
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 8 * * 1"
+jobs:
+  devcontainer-build:
+    uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        py_ver: ["3.9", "3.10"]
+        mysql_ver: ["8.0", "5.7"]
+        include:
+          - py_ver: "3.8"
+            mysql_ver: "5.7"
+          - py_ver: "3.7"
+            mysql_ver: "5.7"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 "black[jupyter]"
+      - name: Run style tests
+        run: |
+          python_version=${{matrix.py_ver}}
+          black element_interface --check --verbose --target-version py${python_version//.}

CHANGELOG.md

@@ -3,12 +3,18 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.7.0] - 2024-08-09
+
++ Add - `memoized_result` decorator to cache function results
++ Update - `prairie_view_loader.py` to create big tiff files from `.ome.tif` files
++ Update - `run_caiman.py` to run latest version of CaImAn
++ Update - `caiman_loader.py` to process output of latest version of CaImAn
++ Fix - general fixes and improvements
 
 ## [0.6.1] - 2023-08-02
 
 + Update DANDI upload funtionality to improve useability
 
-
 ## [0.6.0] - 2023-07-26
 
 + Update - `prairieviewreader.py` -> `prairie_view_loader.py`
@@ -83,6 +89,8 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.
 
+
+[0.7.0]: https://github.com/datajoint/element-interface/releases/tag/0.7.0
 [0.6.0]: https://github.com/datajoint/element-interface/releases/tag/0.6.0
 [0.5.4]: https://github.com/datajoint/element-interface/releases/tag/0.5.4
 [0.5.3]: https://github.com/datajoint/element-interface/releases/tag/0.5.3

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 DataJoint NEURO
+Copyright (c) 2024 DataJoint
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/src/concepts.md

@@ -24,6 +24,12 @@ how to use various Elements.
 `utils.str_to_bool` converts a set of strings to boolean True or False. This is implemented
 as the equivalent item in Python's `distutils` which will be removed in future versions.
 
+`utils.memoized_result` is a decorator that caches the result of a function call based 
+ on input parameters and the state of the output. If the function is called with the same
+ parameters and the output files in the directory remain unchanged, it returns the 
+ cached results; otherwise, it executes the function and caches the new results along 
+ with metadata.
+
 ### Suite2p
 
 This Element provides functions to independently run Suite2p's motion correction,
@@ -46,13 +52,15 @@ Requirements:
 
 ### PrairieView Reader
 
-This Element provides a function to read the PrairieView Scanner's metadata file. The
-PrairieView software generates one `.ome.tif` imaging file per frame acquired. The
-metadata for all frames is contained in one `.xml` file. This function locates the
-`.xml` file and generates a dictionary necessary to populate the DataJoint ScanInfo and
-Field tables. PrairieView works with resonance scanners with a single field, does not
-support bidirectional x and y scanning, and the `.xml` file does not contain ROI
-information.
+This Element provides a `PrairieViewMeta` class to handle different types of output from
+ the PrairieView Scanner. The PrairieView software either generates one `.ome.tif` 
+ imaging file per frame acquired or multi-page `.ome.tif` files. The metadata for all 
+ frames is contained in one `.xml` file. This class contains methods that locate the 
+ `.xml` file and generate a dictionary necessary to populate the DataJoint ScanInfo and
+  Field tables. The class also contains methods to create a big tiff file from the 
+  individual `.ome.tif` files. PrairieView works with resonance scanners with a single 
+  field, does not support bidirectional x and y scanning, and the `.xml` file does not 
+  contain ROI information.
 
 ## Element Architecture
 

docs/src/index.md

@@ -16,4 +16,6 @@ a number of other Elements.
 
 - Data ingestion, see [`ingest_csv_to_table` API](./api/element_interface/utils/#element_interface.utils.ingest_csv_to_table)
 
+- Code execution, see [`memoized_result` API](./api/element_interface/utils/#element_interface.utils.memoized_result)
+
 Visit the [Concepts page](./concepts.md) for more information on these tools.