np_codeocean 0.3.5__tar.gz → 0.3.7__tar.gz

{np_codeocean-0.3.5 → np_codeocean-0.3.7}/PKG-INFO

@@ -1,9 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: np_codeocean
-Version: 0.3.5
+Version: 0.3.7
 Summary: Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
-Author-Email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>, Chris Mochizuki <chrism@alleninstitute.org>, Arjun Sridhar <arjun.sridhar@alleninstitute.org>
+Author-email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>, Chris Mochizuki <chrism@alleninstitute.org>, Arjun Sridhar <arjun.sridhar@alleninstitute.org>
 License: MIT
+Project-URL: Source, https://github.com/AllenInstitute/np_codeocean
+Project-URL: Issues, https://github.com/AllenInstitute/np_codeocean/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
@@ -11,9 +13,8 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX :: Linux
-Project-URL: Source, https://github.com/AllenInstitute/np_codeocean
-Project-URL: Issues, https://github.com/AllenInstitute/np_codeocean/issues
 Requires-Python: >=3.10
+Description-Content-Type: text/markdown
 Requires-Dist: np_session>=0.6.44
 Requires-Dist: np-tools>=0.1.23
 Requires-Dist: np-config>=0.4.33
@@ -27,7 +28,15 @@ Requires-Dist: cryptography<43.0
 Requires-Dist: aind-data-transfer-service>=1.15.0
 Requires-Dist: aind-slurm-rest-v2==0.0.3
 Requires-Dist: aind-codeocean-pipeline-monitor>=0.5.2
-Description-Content-Type: text/markdown
+Provides-Extra: dev
+Requires-Dist: bump>=1.3.2; extra == "dev"
+Provides-Extra: dynamicrouting
+Requires-Dist: npc-lims>=0.1.154; extra == "dynamicrouting"
+Requires-Dist: npc-sessions>=0.0.273; extra == "dynamicrouting"
+Requires-Dist: aind-codeocean-pipeline-monitor[full]>=0.5.0; extra == "dynamicrouting"
+Requires-Dist: aind-metadata-mapper==0.18.2; extra == "dynamicrouting"
+Provides-Extra: openscope
+Requires-Dist: aind-metadata-mapper==0.18.1; extra == "openscope"
 
 # np_codeocean
 Tools for uploading Mindscope Neuropixels experiments to S3 (for Code Ocean).
@@ -35,6 +44,29 @@ Tools for uploading Mindscope Neuropixels experiments to S3 (for Code Ocean).
 Requires running as admin on Windows in order to create remote-to-remote symlinks
 on the Isilon.
 
+## Install 
+For Dynamic Routing:
+```shell
+uv sync --extra dynamicrouting
+```
+
+For OpenScope:
+```shell
+uv sync --extra openscope
+```
+
+## Add dependencies
+For shared utilities:
+```shell
+uv add <package-name>
+```
+
+For Dynamic Routing or OpenScope specific utilities:
+```shell
+uv add <package-name> --optional <dynamicrouting|openscope>
+```
+
+## Usage 
 - `upload` CLI tool is provided, which uses the
   [`np_session`](https://github.com/AllenInstitute/np_session) interface to find
   and upload

{np_codeocean-0.3.5 → np_codeocean-0.3.7}/README.md

@@ -1,28 +1,51 @@
-# np_codeocean
-Tools for uploading Mindscope Neuropixels experiments to S3 (for Code Ocean).
-
-Requires running as admin on Windows in order to create remote-to-remote symlinks
-on the Isilon.
-
-- `upload` CLI tool is provided, which uses the
-  [`np_session`](https://github.com/AllenInstitute/np_session) interface to find
-  and upload
-  raw data for one ecephys session:
-
-    ```
-    pip install np_codeocean
-    upload <session-id>
-    ```
- 
-    where session-id is any valid input to `np_session.Session()`, e.g.: 
-    - a lims ID (`1333741475`) 
-    - a workgroups foldername (`DRPilot_366122_20230101`) 
-    - a path to a session folder (    `\\allen\programs\mindscope\workgroups\np-exp\1333741475_719667_20240227`)
-    
-- a folder of symlinks pointing to the raw data is created, with a new structure suitable for the KS2.5 sorting pipeline on Code Ocean
-- the symlink folder, plus metadata, are entered into a csv file, which is
-  submitted to [`http://aind-data-transfer-service`](http://aind-data-transfer-service), which in turn runs the
-  [`aind-data-transfer`](https://github.com/AllenNeuralDynamics/aind-data-transfer)
-  tool on the HPC, which follows the symlinks to the original data,
-  median-subtracts/scales/compresses ephys data, then uploads with the AWS CLI tool
-- all compression/zipping acts on copies in temporary folders: the original raw data is not altered in anyway 
+# np_codeocean
+Tools for uploading Mindscope Neuropixels experiments to S3 (for Code Ocean).
+
+Requires running as admin on Windows in order to create remote-to-remote symlinks
+on the Isilon.
+
+## Install 
+For Dynamic Routing:
+```shell
+uv sync --extra dynamicrouting
+```
+
+For OpenScope:
+```shell
+uv sync --extra openscope
+```
+
+## Add dependencies
+For shared utilities:
+```shell
+uv add <package-name>
+```
+
+For Dynamic Routing or OpenScope specific utilities:
+```shell
+uv add <package-name> --optional <dynamicrouting|openscope>
+```
+
+## Usage 
+- `upload` CLI tool is provided, which uses the
+  [`np_session`](https://github.com/AllenInstitute/np_session) interface to find
+  and upload
+  raw data for one ecephys session:
+
+    ```
+    pip install np_codeocean
+    upload <session-id>
+    ```
+ 
+    where session-id is any valid input to `np_session.Session()`, e.g.: 
+    - a lims ID (`1333741475`) 
+    - a workgroups foldername (`DRPilot_366122_20230101`) 
+    - a path to a session folder (    `\\allen\programs\mindscope\workgroups\np-exp\1333741475_719667_20240227`)
+    
+- a folder of symlinks pointing to the raw data is created, with a new structure suitable for the KS2.5 sorting pipeline on Code Ocean
+- the symlink folder, plus metadata, are entered into a csv file, which is
+  submitted to [`http://aind-data-transfer-service`](http://aind-data-transfer-service), which in turn runs the
+  [`aind-data-transfer`](https://github.com/AllenNeuralDynamics/aind-data-transfer)
+  tool on the HPC, which follows the symlinks to the original data,
+  median-subtracts/scales/compresses ephys data, then uploads with the AWS CLI tool
+- all compression/zipping acts on copies in temporary folders: the original raw data is not altered in anyway 

{np_codeocean-0.3.5 → np_codeocean-0.3.7}/pyproject.toml

@@ -1,53 +1,7 @@
-[tool.pdm.scripts]
-ruff = "ruff --fix src"
-blue = "blue src"
-pytest = "pytest --cov"
-bump = "bump -p pyproject.toml"
-
-[tool.pdm.scripts.prebuild]
-composite = [
-    "blue",
-    "ruff",
-    "pytest",
-]
-
-[tool.pdm.scripts.build]
-composite = [
-    "prebuild",
-    "pdm build",
-]
-
-[tool.pdm.scripts.dry-run]
-composite = [
-    "prebuild",
-    "pdm build",
-    "pdm publish --no-build --repository https://test.pypi.org/simple",
-]
-
-[tool.pdm.scripts.publish]
-composite = [
-    "prebuild",
-    "bump",
-    "pdm build",
-    "pdm publish --no-build",
-]
-
-[tool.pdm.scripts.pub]
-composite = [
-    "bump",
-    "pdm publish",
-]
-
-[tool.uv]
-package = true
-default-groups = [
-    "dev",
-    "dynamicrouting",
-]
 
 [project]
 name = "np_codeocean"
-version = "0.3.5"
+version = "0.3.7"
 description = "Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean"
 authors = [
     { name = "Ben Hardcastle", email = "ben.hardcastle@alleninstitute.org" },
@@ -93,24 +47,94 @@ upload_dr_behavior = "np_codeocean.scripts.upload_dynamic_routing_behavior:main"
 upload_dr_ecephys = "np_codeocean.scripts.upload_dynamic_routing_ecephys:main"
 upload_sessions = "np_codeocean.scripts.upload_sessions:main"
 
-[dependency-groups]
-dev = [
-    "bump>=1.3.2",
-    "pdm>=2.4.9",
-]
+[project.optional-dependencies]
+dev = ["bump>=1.3.2"]
 dynamicrouting = [
     "npc-lims>=0.1.154",
     "npc-sessions>=0.0.273",
     "aind-codeocean-pipeline-monitor[full]>=0.5.0",
     "aind-metadata-mapper==0.18.2",
-    "npc-mvr>=0.1.14",
-    "npc-stim>=0.1.14",
-    "npc-samstim>=0.1.13",
-    "npc-sync>=0.1.25",
+]
+openscope = [
+    "aind-metadata-mapper==0.18.1",
 ]
 
+[tool.uv]
+conflicts = [
+    [
+      { extra = "dynamicrouting" },
+      { extra = "openscope" },
+    ],
+]
+package = true
+default-groups = "all"
+
+
 [build-system]
-requires = [
-    "pdm-backend",
+requires = ["setuptools>=61", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[dependency-groups]
+task_runner = ["poethepoet>=0.33.1"]
+linting = ["black>=25.1.0", "isort>=6.0.1", "ruff>=0.11.2"]
+testing = ["mypy>=1.4.1"]
+bump = ["bump-my-version>=1.1.1", "git-changelog>=2.5.3"]
+
+
+[tool.poe.tasks]
+mypy = "mypy src --install-types --non-interactive"
+test = ["mypy"]
+ruff = "ruff check src --fix-only"
+black = "black src"
+format = ["ruff", "black"]
+bump_pub_tag = "bump-my-version bump patch"
+release = ["format", "bump_pub_tag"]
+
+[tool.bumpversion]
+tag = true
+allow_dirty = true
+commit = true
+commit_args = "-a"
+message = "Bump version: {current_version} → {new_version} [skip actions]"
+pre_commit_hooks = [
+    "uv lock --upgrade-package np_workflows",
+    "git-changelog -o CHANGELOG.md",
+    "uv build",
+    "uv publish",
+]
+post_commit_hooks = [
+    "git push origin main",
+    "git push --tags",
+]
+
+[tool.ruff]
+line-length = 100
+select = [
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "E",      # pycodestyle
+    "F",      # pyflakes
+    "PGH",    # pygrep-hooks
+    "RUF",    # ruff
+    "W",      # pycodestyle
+    "YTT",    # flake8-2020
+    "ANN",
+    "C",
+    "I",
+    "RUF100",
+    "N",
+    "UP",
 ]
-build-backend = "pdm.backend"
+# extend-ignore = ["B018", "B019"]
+src = ["src"]
+extend-exclude = ["tests/fixtures"]
+target-version = "py39"
+
+[tool.ruff.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.mccabe]
+max-complexity = 10
+
+[tool.ruff.isort]
+known-first-party = ["np_workflows"]

np_codeocean-0.3.7/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

np_codeocean-0.3.7/src/np_codeocean/__init__.py

@@ -0,0 +1,2 @@
+from np_codeocean.np_session_utils import *
+from np_codeocean.utils import *

{np_codeocean-0.3.5 → np_codeocean-0.3.7}/src/np_codeocean/metadata/__init__.py

@@ -1,3 +1,3 @@
 """
 Migrated from https://github.com/AllenInstitute/np-aind-metadata
-"""
+"""

{np_codeocean-0.3.5 → np_codeocean-0.3.7}/src/np_codeocean/metadata/common.py

@@ -1,6 +1,4 @@
-
-"""Models and controlled language for aind-data-schema devices names.
-"""
+"""Models and controlled language for aind-data-schema devices names."""
 
 import typing