From 838f04cad73a1e925d7a9802905807d427463933 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Tue, 7 Oct 2025 18:30:07 +0100 Subject: [PATCH 1/6] refactor: move element-deeplabcut to optional dependencies --- pyproject.toml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 5283b79a..070a28f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,12 +29,22 @@ dependencies = [ ] [project.optional-dependencies] + +deeplabcut = [ + "element-deeplabcut @ git+https://github.com/datajoint/element-deeplabcut.git", +] + elements = [ "element-lab @ git+https://github.com/datajoint/element-lab.git", "element-session @ git+https://github.com/datajoint/element-session.git", "element-interface @ git+https://github.com/datajoint/element-interface.git", "element-animal @ git+https://github.com/datajoint/element-animal.git", ] + +all = [ + "element-moseq[moseq,deeplabcut,elements]", +] + tests = [ "pytest", "pytest-cov", From 61e94b77a509885b6a02369a595d4ebae54b5f40 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Tue, 7 Oct 2025 18:32:12 +0100 Subject: [PATCH 2/6] chore: bump version and update CHANGELOG --- CHANGELOG.md | 3 +++ element_moseq/version.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c02e358f..0796f50b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,9 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention. +## [1.0.2] - 2025-10-07 ++ Update - Move `element-deeplabcut` as optional dependency to avoid circular dependencies + ## [1.0.1] - 2025-09-23 + Feat - Add support to generate PNG version of fitting progress plots in `PreFit`, `FullFit`, and `moseq_report` schema + Fix - Update path handling to use `Path` objects and `dj.logger` diff --git a/element_moseq/version.py b/element_moseq/version.py index 831333b5..0a69f742 100644 --- a/element_moseq/version.py +++ b/element_moseq/version.py @@ -2,4 +2,4 @@ Package metadata """ -__version__ = "1.0.1" +__version__ = "1.0.2" From c8d3581183c78128eb74091ce9dbf8b55e537233 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Tue, 7 Oct 2025 18:41:07 +0100 Subject: [PATCH 3/6] minor typo --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 070a28f4..a36fbc28 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,16 +41,16 @@ elements = [ "element-animal @ git+https://github.com/datajoint/element-animal.git", ] -all = [ - "element-moseq[moseq,deeplabcut,elements]", -] - tests = [ "pytest", "pytest-cov", "shutils", ] +all = [ + "element-moseq[deeplabcut,elements,tests]", +] + [project.urls] Homepage = "https://github.com/datajoint/element-moseq" Repository = "https://github.com/datajoint/element-moseq" From a2d241bda86673f93cad7609fd77f16e41abbf18 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Wed, 8 Oct 2025 01:54:09 +0100 Subject: [PATCH 4/6] update README --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 2e01e916..c38576ac 100644 --- a/README.md +++ b/README.md @@ -22,10 +22,18 @@ DataJoint Elements collectively standardize and automate data collection and ana git clone https://github.com//element-moseq.git ``` ++ Install [Conda](https://docs.conda.io/en/latest/miniconda.html). + ++ Create and activate a Conda environment: + ```bash + conda env create -f conda_env.yml + conda activate element_moseq + ``` + + Install with `pip`: ```bash - pip install -e .[keypoint-moseq] + pip install -e .[kpms_cpu] # MacOS: pip install -e ".[kpms_cpu]" ``` + [Interactive tutorial on GitHub Codespaces](https://github.com/datajoint/element-moseq#interactive-tutorial) From 03bb3b34460872fb2ac8bf9525b18424cb24e52d Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Wed, 8 Oct 2025 01:55:21 +0100 Subject: [PATCH 5/6] chore: add different optional dependencies for kpms cpu/gpu --- pyproject.toml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d76908fb..1bdd81f3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,7 +39,9 @@ elements = [ "element-interface @ git+https://github.com/datajoint/element-interface.git", "element-animal @ git+https://github.com/datajoint/element-animal.git", ] -kpms = ["jax<0.7.0", "keypoint-moseq @ git+https://github.com/dattalab/keypoint-moseq.git"] +kpms_cpu = ["jax<0.7.0", "keypoint-moseq @ git+https://github.com/dattalab/keypoint-moseq.git"] +kpms_gpu = ["jax<0.7.0", "keypoint-moseq[cuda] @ git+https://github.com/dattalab/keypoint-moseq.git"] + tests = [ "pytest", "pytest-cov", From adf55c85367b075df92a0ad8deb98b16683092d3 Mon Sep 17 00:00:00 2001 From: MilagrosMarin Date: Wed, 8 Oct 2025 02:17:27 +0100 Subject: [PATCH 6/6] revert a few updates --- pyproject.toml | 9 --------- 1 file changed, 9 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1bdd81f3..e2a16bda 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,11 +28,6 @@ dependencies = [ ] [project.optional-dependencies] - -deeplabcut = [ - "element-deeplabcut @ git+https://github.com/datajoint/element-deeplabcut.git", -] - elements = [ "element-lab @ git+https://github.com/datajoint/element-lab.git", "element-session @ git+https://github.com/datajoint/element-session.git", @@ -48,10 +43,6 @@ tests = [ "shutils", ] -all = [ - "element-moseq[deeplabcut,elements,tests]", -] - [project.urls] Homepage = "https://github.com/datajoint/element-moseq" Repository = "https://github.com/datajoint/element-moseq"