hoa-tools 1.0__tar.gz → 1.0.1__tar.gz

hoa_tools-1.0.1/.github/workflows/publish.yml

@@ -0,0 +1,52 @@
+name: Publish
+
+on: push
+
+jobs:
+  build:
+    name: build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install pypa/build
+        run: python -m pip install build --user
+
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      publish
+    if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/hoa-tools # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

{hoa_tools-1.0 → hoa_tools-1.0.1}/.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.4
+    rev: v0.11.6
     hooks:
       - id: ruff
       - id: ruff-format

{hoa_tools-1.0 → hoa_tools-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoa-tools
-Version: 1.0
+Version: 1.0.1
 Summary: Tools for working with the Human Organ Atlas
 Author-email: David Stansby <d.stansby@ucl.ac.uk>
 License: Copyright (c) 2024, David Stansby

{hoa_tools-1.0 → hoa_tools-1.0.1}/docs/development.md

@@ -2,12 +2,10 @@
 
 ## Updating the inventory
 
-To update the version of the inventory, update the git submodule at src/hoa_tools/data/metadata.
+To update the version of the inventory, update the git submodule at `src/hoa_tools/data/metadata`.
 The inventory is stored separately at https://github.com/HumanOrganAtlas/metadata-schemas.
 
-## Generating the data model
-
-Using [datamodel-code-generator](https://github.com/koxudaxi/datamodel-code-generator/):
+Then update the Python data model using [datamodel-code-generator](https://github.com/koxudaxi/datamodel-code-generator/):
 
 ```
 datamodel-codegen --input src/hoa_tools/data/metadata/metadata-schema.json --input-file-type jsonschema --output src/hoa_tools/metadata.py --output-model-type pydantic_v2.BaseModel --use-annotated --enum-field-as-literal all --use-union-operator --use-standard-collections

hoa_tools-1.0.1/docs/release-notes.md

@@ -0,0 +1,10 @@
+# Release notes
+
+## 1.0.1
+
+- Updated the metadata database to version 1.0. This has no major differences
+  from the previous version of the metadata database (version 0.9).
+
+## 1.0
+
+First release of the `hoa-tools` package 🚀

{hoa_tools-1.0 → hoa_tools-1.0.1}/src/hoa_tools/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.0'
-__version_tuple__ = version_tuple = (1, 0)
+__version__ = version = '1.0.1'
+__version_tuple__ = version_tuple = (1, 0, 1)

{hoa_tools-1.0 → hoa_tools-1.0.1}/src/hoa_tools/metadata.py

@@ -1,6 +1,6 @@
 # generated by datamodel-codegen:
 #   filename:  metadata-schema.json
-#   timestamp: 2025-04-10T13:29:59+00:00
+#   timestamp: 2025-04-25T10:05:35+00:00
 
 from __future__ import annotations
 
@@ -601,8 +601,10 @@ class Scan(BaseModel):
             "Gadox 60um",
             "CSI trixell structured 650um, 5um pitch",
             "GGG 8um",
-            "gagg1000_refl",
-            "dual-lso5000_refl",
+            "GGG 20um",
+            "GAGG 1000um, reflective",
+            "GAGG 100um, reflective",
+            "Dual LySO:Ce 5000um, reflective",
         ]
         | None,
         Field(
@@ -760,6 +762,6 @@ class HOAMetadata(BaseModel):
     ] = None
     citation: Annotated[Citation, Field(title="Dataset citation")]
     metadata_version: Annotated[
-        Literal["0.9"],
+        Literal["1.0"],
         Field(description="Version of this metadata file.", title="Metadata Version"),
-    ] = "0.9"
+    ] = "1.0"

{hoa_tools-1.0 → hoa_tools-1.0.1}/src/hoa_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoa-tools
-Version: 1.0
+Version: 1.0.1
 Summary: Tools for working with the Human Organ Atlas
 Author-email: David Stansby <d.stansby@ucl.ac.uk>
 License: Copyright (c) 2024, David Stansby

hoa_tools-1.0.1/src/hoa_tools.egg-info/SOURCES.txt

@@ -0,0 +1,53 @@
+.gitignore
+.gitmodules
+.pre-commit-config.yaml
+.readthedocs.yml
+CITATION.cff
+LICENSE.md
+MANIFEST.in
+README.md
+mkdocs.yml
+pyproject.toml
+ruff.toml
+.github/dependabot.yml
+.github/workflows/publish.yml
+.github/workflows/tests.yml
+.vscode/settings.json
+docs/development.md
+docs/how_to.md
+docs/index.md
+docs/release-notes.md
+docs/api/dataset.md
+docs/api/index.md
+docs/api/inventory.md
+docs/api/metadata.md
+docs/api/types.md
+docs/api/voi.md
+docs/tutorial/dataset.py
+docs/tutorial/fetching_data.py
+docs/tutorial/index.md
+docs/tutorial/inventory.py
+docs/tutorial/registration.py
+docs/tutorial/vois.py
+schemas/github-issue-forms.json
+src/hoa_tools/__init__.py
+src/hoa_tools/_n5.py
+src/hoa_tools/_version.py
+src/hoa_tools/dataset.py
+src/hoa_tools/inventory.py
+src/hoa_tools/metadata.py
+src/hoa_tools/py.typed
+src/hoa_tools/registration.py
+src/hoa_tools/types.py
+src/hoa_tools/voi.py
+src/hoa_tools.egg-info/PKG-INFO
+src/hoa_tools.egg-info/SOURCES.txt
+src/hoa_tools.egg-info/dependency_links.txt
+src/hoa_tools.egg-info/requires.txt
+src/hoa_tools.egg-info/top_level.txt
+tests/test_dataset.py
+tests/test_inventory.py
+tests/test_registration.py
+tests/test_voi.py
+tests/cassettes/test_remote_array.yaml
+tests/cassettes/test_remote_array_zarr.yaml

hoa_tools-1.0/docs/release-notes.md

@@ -1,5 +0,0 @@
-# Release notes
-
-## 1.0
-
-First release of the `hoa-tools` package 🚀

hoa_tools-1.0/src/hoa_tools/data/metadata/metadata/A186_lung_right_VOI-3_4.26um_bm18.json

@@ -1,275 +0,0 @@
-{
-  "name": "A186_lung_right_VOI-3_4.26um_bm18",
-  "dataset_type": "zoom",
-  "voi": "VOI-3",
-  "data": {
-    "shape": [6048, 6048, 4802],
-    "voxel_size_um": 4.26,
-    "gcs_url": "zarr://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/A186/lung-right/4.26um_VOI-3_bm18.ome.zarr/"
-  },
-  "sample": {
-    "organ": "lung",
-    "organ_context": "right",
-    "post_mortem_interval_hours": null,
-    "fixation_method": null,
-    "fixation_medium": null,
-    "organ_infilled": null,
-    "stabilisation_medium": null,
-    "degassing_method": null,
-    "scan_solvent": null,
-    "scan_solvent_concentration": null,
-    "scan_temperature": "room temperature"
-  },
-  "donor": {
-    "id": "A186",
-    "age": null,
-    "sex": null,
-    "weight": null,
-    "height": null,
-    "cause_of_death": "not applicable - transplant organ",
-    "date_of_death": null,
-    "medical_history": "lung from patient with PVOD",
-    "diabetes": null,
-    "hypertension": null,
-    "smoker": null
-  },
-  "scan": {
-    "date": "2024-07-13",
-    "beamline": "BM18",
-    "energy": 90.0,
-    "current_start": 195.004562,
-    "filling_mode": "7/8 multibunch",
-    "n_frames": 9000,
-    "n_ref": 1,
-    "n_dark": 3,
-    "latency_time": 0.004,
-    "exposure_time": 0.04,
-    "subframe_time": 0.04,
-    "n_subframes": 1,
-    "scan_type": "helical",
-    "scan_range": 1800.0,
-    "n_scans": 1,
-    "acquisition": "half",
-    "z_step": null,
-    "scan_time": 397.158199,
-    "filters": ["Sapphire 5mm", "Silver 0.1mm"],
-    "scintillator": "LuAG:Ce 100um, reflective",
-    "optic": "Fixed x1",
-    "optic_magnification": 1.0,
-    "distance_source_sample": 178000.0,
-    "distance_sample_detector": 4000.0,
-    "sensor_name": "Iris15",
-    "sensor_mode": null,
-    "sensor_roi_x_size": 5056,
-    "sensor_roi_y_size": 1400,
-    "sensor_binning": [1, 1],
-    "pixel_size": 4.259,
-    "xray_magnification": 1.022472,
-    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
-    "experiment_type": "Tomography"
-  },
-  "proposal": {
-    "proposal_number": "md1389",
-    "title": "HUB Proposal: Human Organ Atlas Hub (HOAHub)",
-    "proposers": [
-      "Peter Lee",
-      "Claire Walsh",
-      "Anastasia Yendiki",
-      "Maximilian Ackermann",
-      "Alexandre Bellier",
-      "Bernadette De Bakker",
-      "Paul Tafforeau",
-      "Danny Jonigk",
-      "Stijn Verleden"
-    ]
-  },
-  "registration": {
-    "source_dataset": "A186_lung_right_VOI-3_4.26um_bm18",
-    "target_dataset": "A186_lung_right_complete-organ_24.132um_bm18",
-    "translation": [3062.52288443756, 4793.330916908064, 7701.397091020416],
-    "rotation": 5.900206653858209,
-    "scale": 0.17652928005995408
-  },
-  "citation": {
-    "title": "Zoom (VOI-3) at 4.26um of the lung of donor A186, scanned at ESRF on beamline BM18.",
-    "contributors": [
-      {
-        "first_name": "The",
-        "last_name": "Human Organ Atlas Collaboration",
-        "orcid": null,
-        "roles": []
-      },
-      {
-        "first_name": "Alexandre",
-        "last_name": "Bellier",
-        "orcid": "0000-0003-0907-0315",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Anastasia",
-        "last_name": "Yendiki",
-        "orcid": null,
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Andrew",
-        "last_name": "Keenlyside",
-        "orcid": "0000-0002-6059-2103",
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Bernadette",
-        "last_name": "De Bakker",
-        "orcid": null,
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Birger",
-        "last_name": "Tielemans",
-        "orcid": "0000-0002-1775-1797",
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Claire",
-        "last_name": "Walsh",
-        "orcid": "0000-0003-3769-3392",
-        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
-      },
-      {
-        "first_name": "Daisuke",
-        "last_name": "Yamada",
-        "orcid": "0000-0003-1561-5908",
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Danny",
-        "last_name": "Jonigk",
-        "orcid": "0000-0002-5251-2281",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "David",
-        "last_name": "Stansby",
-        "orcid": "0000-0002-1365-1908",
-        "roles": ["Data curation", "Investigation", "Software"]
-      },
-      {
-        "first_name": "Guillaume",
-        "last_name": "Gaisne",
-        "orcid": "0000-0002-3401-7930",
-        "roles": ["Data curation", "Software"]
-      },
-      {
-        "first_name": "Hector",
-        "last_name": "Dejea I Velardo",
-        "orcid": "0000-0003-2584-9812",
-        "roles": ["Data curation", "Investigation"]
-      },
-      {
-        "first_name": "Jana",
-        "last_name": "Dietrich",
-        "orcid": null,
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Joanna",
-        "last_name": "Purzycka",
-        "orcid": "0000-0001-8742-5279",
-        "roles": ["Data curation"]
-      },
-      {
-        "first_name": "Joseph",
-        "last_name": "Brunet",
-        "orcid": "0000-0002-8424-9510",
-        "roles": ["Data curation", "Investigation", "Software"]
-      },
-      {
-        "first_name": "Joseph",
-        "last_name": "Jacob",
-        "orcid": "0000-0002-8054-2293",
-        "roles": ["Resources"]
-      },
-      {
-        "first_name": "Mark",
-        "last_name": "Kuehnel",
-        "orcid": "0000-0003-3558-2576",
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Matthieu",
-        "last_name": "Chourrout",
-        "orcid": "0000-0002-2282-6976",
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Maximilian",
-        "last_name": "Ackermann",
-        "orcid": "0000-0001-9996-2477",
-        "roles": ["Funding acquisition", "Resources"]
-      },
-      {
-        "first_name": "Mei",
-        "last_name": "Yang",
-        "orcid": "0009-0005-4035-0966",
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Paul",
-        "last_name": "Tafforeau",
-        "orcid": "0000-0002-5962-1683",
-        "roles": [
-          "Conceptualization",
-          "Data curation",
-          "Funding acquisition",
-          "Investigation"
-        ]
-      },
-      {
-        "first_name": "Peter",
-        "last_name": "Lee",
-        "orcid": "0000-0002-3898-8881",
-        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
-      },
-      {
-        "first_name": "Stijn",
-        "last_name": "Verleden",
-        "orcid": "0000-0002-9656-5844",
-        "roles": ["Funding acquisition", "Resources"]
-      },
-      {
-        "first_name": "Theresa",
-        "last_name": "Urban",
-        "orcid": "0000-0002-0352-8180",
-        "roles": ["Data curation", "Investigation", "Software"]
-      }
-    ],
-    "doi": null,
-    "author_list": [
-      "The Human Organ Atlas Collaboration",
-      "Alexandre Bellier",
-      "Anastasia Yendiki",
-      "Andrew Keenlyside",
-      "Bernadette De Bakker",
-      "Birger Tielemans",
-      "Claire Walsh",
-      "Daisuke Yamada",
-      "Danny Jonigk",
-      "David Stansby",
-      "Guillaume Gaisne",
-      "Hector Dejea I Velardo",
-      "Jana Dietrich",
-      "Joanna Purzycka",
-      "Joseph Brunet",
-      "Joseph Jacob",
-      "Mark Kuehnel",
-      "Matthieu Chourrout",
-      "Maximilian Ackermann",
-      "Mei Yang",
-      "Paul Tafforeau",
-      "Peter Lee",
-      "Stijn Verleden",
-      "Theresa Urban"
-    ]
-  },
-  "metadata_version": "0.9"
-}