From 70108e4c0a77715806ebcc17849ffabf7ae744f4 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 17 May 2024 04:56:26 +0200 Subject: [PATCH 1/9] fix docs --- docs/mkdocs.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/mkdocs.yaml b/docs/mkdocs.yaml index f162929..7b8aa79 100644 --- a/docs/mkdocs.yaml +++ b/docs/mkdocs.yaml @@ -28,7 +28,7 @@ nav: # 02. Instead of designating codeblocks with bash, use console. For example.. # ```console # cd ../my_dir -# ``` +# ``` # 03. Links across docs should ... # A. Not involve line breaks. # B. Use relative paths to docs in the same repo @@ -48,15 +48,15 @@ nav: # HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build # ``` # 02. The API section will pull docstrings. -# A. Follow google styleguide e.g., +# A. Follow google styleguide e.g., # https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html # With typing suggestions: https://docs.python.org/3/library/typing.html # B. To pull a specific workflow fork, change ./docs/src/api/make_pages.py#L19 # 03. To see your fork of the workflow-{element} in this render, change the # URL in ./docs/src/api/make_pages.py#L19 to your fork. -# 04. To deploy this site on your fork, +# 04. To deploy this site on your fork, # A. declare a branch called gh-pages -# B. go to the your fork > settings > pages +# B. go to the your fork > settings > pages # C. direct pages to render from the gh-pages branch at root # D. push a tag to your fork with the format test*.*.* # @@ -93,13 +93,14 @@ plugins: default_handler: python handlers: python: + paths: [../] options: members_order: source group_by_category: false line_length: 88 - gen-files: scripts: - - ./src/api/make_pages.py + - ./src/api/make_pages.py - literate-nav: nav_file: navigation.md - exclude-search: @@ -172,7 +173,7 @@ extra_css: - assets/stylesheets/extra.css extra_javascript: - - https://js-na1.hs-scripts.com/23133402.js # HubSpot chatbot + - https://js-na1.hs-scripts.com/23133402.js # HubSpot chatbot - javascripts/mathjax.js - https://polyfill.io/v3/polyfill.min.js?features=es6 - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js From eb5db5db49916532fcc60ce059820cc2a66aa1a9 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 18:35:37 +0100 Subject: [PATCH 2/9] refactor(setup): move installation of kpms as `extras_require` for consistency with other elements --- setup.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index b549e09..8a3b8c5 100644 --- a/setup.py +++ b/setup.py @@ -29,11 +29,12 @@ "ipykernel>=6.0.1", "opencv-python", "scipy<1.12.0", - "pydot==2.0", "element-interface @ git+https://github.com/datajoint/element-interface.git", - "keypoint-moseq @ git+https://github.com/dattalab/keypoint-moseq.git", ], extras_require={ + "kpms": [ + "keypoint-moseq @ git+https://github.com/dattalab/keypoint-moseq.git", + ], "elements": [ "element-animal @ git+https://github.com/datajoint/element-animal.git", "element-event @ git+https://github.com/datajoint/element-event.git", From fd824f2f7407340ac3bd2177a150daaceb9002f3 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 18:36:58 +0100 Subject: [PATCH 3/9] update Dockerfile with extras_require --- .devcontainer/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 7e0909d..451f9d7 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -34,7 +34,7 @@ RUN \ apt-get update && \ apt-get install -y gcc ffmpeg graphviz && \ pip install ipywidgets && \ - pip install --no-cache-dir -e /tmp/element-moseq[elements,tests] && \ + pip install --no-cache-dir -e /tmp/element-moseq[kpms,elements,tests] && \ # clean up rm -rf /tmp/element-moseq/ && \ apt-get clean From a09325e94231a37eb03884bb7812d60b5964b8dc Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 18:38:07 +0100 Subject: [PATCH 4/9] update Dockerfile with latest installation of kpms --- .devcontainer/Dockerfile | 3 --- 1 file changed, 3 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 451f9d7..817d2ad 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -39,9 +39,6 @@ RUN \ rm -rf /tmp/element-moseq/ && \ apt-get clean -# Install Keypoint-MoSeq (CPU version) -RUN pip install "jax[cpu]==0.3.22" -f https://storage.googleapis.com/jax-releases/jax_releases.html - ENV DJ_HOST fakeservices.datajoint.io ENV DJ_USER root ENV DJ_PASS simple From b3f075b2c701d180a4be13385eb3052de7c9469e Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 18:42:47 +0100 Subject: [PATCH 5/9] update version and changelog --- CHANGELOG.md | 6 ++++++ element_moseq/version.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f85e1a4..92be8fe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention. +## [0.2.1] - 2024-08-30 + ++ Fix - documentation website ++ Update - `setup.py` with `kpms` installation as `extras_require` for consistency with other Elements ++ Update - Dockerfile + ## [0.2.0] - 2024-08-16 + Add - `load` functions and new secondary attributes for tutorial purposes + Add - `outbox` results in the public s3 bucket to be mounted in Codespaces diff --git a/element_moseq/version.py b/element_moseq/version.py index fb6bf8d..72a028d 100644 --- a/element_moseq/version.py +++ b/element_moseq/version.py @@ -2,4 +2,4 @@ Package metadata """ -__version__ = "0.2.0" +__version__ = "0.2.1" From ae2a596d1d63e22cb38968b881a37848ae551c73 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 18:53:16 +0100 Subject: [PATCH 6/9] udpate Dockerfile --- .devcontainer/Dockerfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 817d2ad..e8b6159 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -39,6 +39,9 @@ RUN \ rm -rf /tmp/element-moseq/ && \ apt-get clean +# Install CPU version for KPMS +RUN pip install "jax[cpu]==0.3.22" -f https://storage.googleapis.com/jax-releases/jax_releases.html + ENV DJ_HOST fakeservices.datajoint.io ENV DJ_USER root ENV DJ_PASS simple From 8268ea27531c3e121fd5e98bb945c70f8acd2296 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 19:54:32 +0100 Subject: [PATCH 7/9] update markdown in docs/src --- docs/src/citation.md | 4 +--- docs/src/index.md | 2 +- docs/src/partnerships.md | 2 +- docs/src/pipeline.md | 4 ++-- 4 files changed, 5 insertions(+), 7 deletions(-) diff --git a/docs/src/citation.md b/docs/src/citation.md index 01252ff..b23d895 100644 --- a/docs/src/citation.md +++ b/docs/src/citation.md @@ -13,6 +13,4 @@ If your work uses the following resources, please cite the respective manuscript + Weinreb C, Pearl J, Lin S, Osman MAM, Zhang L, Annapragada S, Conlin E, Hoffman R, Makowska S, Gillis WF and Jay M. Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics. BioRxiv. 2023 Dec 23. doi: https://doi.org/10.1101/2023.03.16.532307 - + Wiltschko AB, Johnson MJ, Iurilli G, Peterson RE, Katon JM, Pashkovski SL, Abraira VE, - Adams RP, Datta SR. Mapping sub-second structure in mouse behavior. Neuron. 2015 Dec 16; - 88(6):1121-35. \ No newline at end of file + + Wiltschko AB, Johnson MJ, Iurilli G, Peterson RE, Katon JM, Pashkovski SL, Abraira VE, Adams RP, Datta SR. Mapping sub-second structure in mouse behavior. Neuron. 2015 Dec 16;88(6):1121-35. \ No newline at end of file diff --git a/docs/src/index.md b/docs/src/index.md index f111209..f88bc7d 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -29,7 +29,7 @@ combined with other Elements to assemble a fully functional pipeline. + Install with `pip` ```bash - pip install -e . + pip install . ``` + [Data Pipeline](./pipeline.md) - Pipeline and table descriptions diff --git a/docs/src/partnerships.md b/docs/src/partnerships.md index 14efd4e..117621c 100644 --- a/docs/src/partnerships.md +++ b/docs/src/partnerships.md @@ -1,3 +1,3 @@ # Key partnerships -Element MoSeq was developed in collaboration with the [Keypoint-MoSeq developers](https://github.com/dattalab/keypoint-moseq), particularly with Kai Fox from Datta's Lab at Harvard Medical School, to foster integration and interoperability between Keypoint-MoSeq and the DataJoint Element MoSeq. +Element MoSeq was developed in collaboration with the [Keypoint-MoSeq developers](https://github.com/dattalab/keypoint-moseq), particularly with Kai Fox from Datta's Lab at Harvard Medical School, to foster integration and interoperability between Keypoint-MoSeq and the DataJoint Element-MoSeq. diff --git a/docs/src/pipeline.md b/docs/src/pipeline.md index 57458b1..b9c5e4f 100644 --- a/docs/src/pipeline.md +++ b/docs/src/pipeline.md @@ -49,9 +49,9 @@ The Element is composed of two main schemas, `moseq_train` and `moseq_infer`. Th | --- | --- | | Session | Unique experimental session identifier | -### `model_train` schema +### `moseq_train` schema -- For further details see the [`model_train` schema API docs](https://datajoint.com/docs/elements/element-moseq/latest/api/element_moseq/model_train/) +- For further details see the [`moseq_train` schema API docs](https://datajoint.com/docs/elements/element-moseq/latest/api/element_moseq/moseq_train/) | Table | Description | | --- | --- | From 1b5c98bf0317a12cbdc6a30c681439fc12f90c4d Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 19:55:45 +0100 Subject: [PATCH 8/9] fix `reader` module as package and can be imported properly --- element_moseq/readers/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 element_moseq/readers/__init__.py diff --git a/element_moseq/readers/__init__.py b/element_moseq/readers/__init__.py new file mode 100644 index 0000000..e69de29 From 5a587106447f832e1a5f578139f7b060d8656502 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Fri, 30 Aug 2024 20:03:04 +0100 Subject: [PATCH 9/9] update CHANGELOG --- CHANGELOG.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 92be8fe..6a6a148 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,10 +4,11 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention. ## [0.2.1] - 2024-08-30 - -+ Fix - documentation website -+ Update - `setup.py` with `kpms` installation as `extras_require` for consistency with other Elements -+ Update - Dockerfile ++ Fix - `mkdocs` build issues ++ Fix - `reader` module imports by adding `__init__.py` ++ Fix - Move KPMS installation to `extras_require` in `setup` for consistency with other Elements ++ Update - markdown files in `mkdocs` ++ Update- Dockerfile ## [0.2.0] - 2024-08-16 + Add - `load` functions and new secondary attributes for tutorial purposes