From e2887321864057b5169d56302dcf21f77af58639 Mon Sep 17 00:00:00 2001 From: Kyu Hyun Lee Date: Thu, 1 Sep 2022 15:05:01 -0700 Subject: [PATCH 1/4] Update pyproject.toml --- CITATION.cff | 4 ++-- bin/spyglass | 6 ----- pyproject.toml | 60 ++++++++++++++++++++++++++++++++++++++++++++++++-- setup.cfg | 28 ----------------------- 4 files changed, 60 insertions(+), 38 deletions(-) delete mode 100755 bin/spyglass diff --git a/CITATION.cff b/CITATION.cff index f559251f2..a7767f18a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -10,6 +10,6 @@ authors: - family-names: "Frank" given-names: "Loren" title: "spyglass" -version: 0.3.0 -date-released: 2020-12-18 +version: 0.1.0 +date-released: 2022-9-1 url: "https://github.com/LorenFrankLab/spyglass" \ No newline at end of file diff --git a/bin/spyglass b/bin/spyglass deleted file mode 100755 index 0f6d92b7a..000000000 --- a/bin/spyglass +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env python3 - -from spyglass.cli import cli - -if __name__ == '__main__': - cli() \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index b5a3c468d..500751ceb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,62 @@ [build-system] requires = [ - "setuptools>=42", + "setuptools>=61.0", "wheel" ] -build-backend = "setuptools.build_meta" \ No newline at end of file +build-backend = "setuptools.build_meta" + +[project] +name = "spyglass" +version = "0.1.0" +authors = [ + { name="Loren Frank", email="loren.frank@ucsf.edu" }, + { name="Kyu Hyun Lee", email="kyuhyun.lee@ucsf.edu" }, + { name="Eric Denovellis", email="eric.denovellis@ucsf.edu" }, + { name="Ryan Ly", email="rly@lbl.gov" } +] +description = "Neuroscience data analysis framework for reproducible research" +readme = "README.md" +license = { file="LICENSE" } +requires-python = ">=3.8" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", +] +keywords = ["neuroscience", "research", "electrophysiology", "reproducible", "data analysis", + "spike sorting", "spikeinterface","datajoint", "nwb", "kachery", "sortingview"] +dependencies = [ + "jupyterlab>=3.*", + "pydotplus>=2.0.*", + "dask>=2.30", + "position_tools", + "track_linearization", + "replay_trajectory_classification", + "ripple_detection", + "trajectory_analysis_tools", + "matplotlib", + "seaborn", + "skan", + "bottleneck", + "ipympl", + "tqdm", + "pubnub<6.4.0", + "mountainsort4", + "pynwb>=2.0.0,<3", + "hdmf>=3.4.2", + "datajoint>=0.13.6", + "ghostipy", + "pymysql>=1.0.*", + "sortingview>=0.8", + "pyyaml", + "click", + "spikeinterface @ git+https://github.com/SpikeInterface/spikeinterface@master#egg=spikeinterface", + "ndx_franklab_novela @ git+https://github.com/LorenFrankLab/ndx-franklab-novela@master#egg=ndx_franklab_novela" +] + +[project.scripts] +spyglass_cli = "spyglass.cli:cli" + +[project.urls] +"Homepage" = "https://github.com/LorenFrankLab/spyglass" +"Bug Tracker" = "https://github.com/LorenFrankLab/spyglass/issues" diff --git a/setup.cfg b/setup.cfg index b28bf7595..2455897c8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,31 +1,3 @@ -[metadata] -name = spyglass -version = 0.3.1 -author = Loren Frank, Kyu Hyun Lee, Eric Denovellis, Ryan Ly -author_email = loren@phy.ucsf.edu -description = Neuroscience data pipeline for reproducible research by Loren Frank Lab, UCSF -long_description = file: README.md -long_description_content_type = text/markdown -license_files = LICENSE -url = https://github.com/LorenFrankLab/spyglass -project_urls = - Bug Tracker = https://github.com/LorenFrankLab/spyglass/issues -classifiers = - Programming Language :: Python :: 3 - License :: OSI Approved :: MIT License - Operating System :: OS Independent - -[options] -package_dir = - = src -packages = find: -python_requires = >=3.8 -scripts = - bin/spyglass - -[options.packages.find] -where = src - [flake8] max-line-length = 120 max-complexity = 17 From e5c1a835223ba5f44feb5a7fa851c1c8c039989f Mon Sep 17 00:00:00 2001 From: Kyu Hyun Lee Date: Thu, 1 Sep 2022 15:41:21 -0700 Subject: [PATCH 2/4] Include tests --- MANIFEST.in | 2 ++ pyproject.toml | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 MANIFEST.in diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 000000000..80d188209 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,2 @@ +graft tests +global-exclude *.py[cod] \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 500751ceb..8f12bb12a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,7 +50,7 @@ dependencies = [ "sortingview>=0.8", "pyyaml", "click", - "spikeinterface @ git+https://github.com/SpikeInterface/spikeinterface@master#egg=spikeinterface", + "spikeinterface", "ndx_franklab_novela @ git+https://github.com/LorenFrankLab/ndx-franklab-novela@master#egg=ndx_franklab_novela" ] From 306bada6af96ad66dcfe8efd965ed143f123467f Mon Sep 17 00:00:00 2001 From: Kyu Hyun Lee Date: Thu, 1 Sep 2022 16:02:47 -0700 Subject: [PATCH 3/4] Update readme --- README.md | 8 -------- pyproject.toml | 2 +- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/README.md b/README.md index 82927597c..99d596357 100644 --- a/README.md +++ b/README.md @@ -47,14 +47,6 @@ Step 1 below only applies if you are a member of Frank lab at UCSF. If you're no export DJ_SUPPORT_FILEPATH_MANAGEMENT="TRUE" ``` Note that a local SPYGLASS_TEMP_DIR (e.g. one on your machine) will speed up spike sorting, but make sure it has enough free space (ideally at least 500GB) - - If you also want to enable file sharing of franklab files through kachery-cloud, add the following - ```bash - export KACHERY_CLOUD_DIR="/stelmo/nwb/.kachery-cloud" - export KACHERY_CLOUD_PROJECT=lqqrbobsev - ``` - - Additional instructions for setting up sharing can be found in the main documentation (TODO) 3. Configure `DataJoint`. To connect to the database, you need to specify information such as the hostname and the port. You should also change your password from the temporary one you were given. Go to the config directory, and run [`dj_config.py`](https://github.com/LorenFrankLab/spyglass/blob/master/config/dj_config.py) in the terminal with your username: diff --git a/pyproject.toml b/pyproject.toml index 8f12bb12a..25bee3463 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -51,7 +51,7 @@ dependencies = [ "pyyaml", "click", "spikeinterface", - "ndx_franklab_novela @ git+https://github.com/LorenFrankLab/ndx-franklab-novela@master#egg=ndx_franklab_novela" + "ndx_franklab_novela>=0.1.0" ] [project.scripts] From 14362e7c60d03e7aa1e652e2364b6a84651ef270 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 1 Sep 2022 16:57:53 -0700 Subject: [PATCH 4/4] Fix date released --- CITATION.cff | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index a7767f18a..3f6d7a5c7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -11,5 +11,5 @@ authors: given-names: "Loren" title: "spyglass" version: 0.1.0 -date-released: 2022-9-1 -url: "https://github.com/LorenFrankLab/spyglass" \ No newline at end of file +date-released: 2022-09-01 +url: "https://github.com/LorenFrankLab/spyglass"