Merge pull request #15 from int-brain-lab/0.5.5

0.5.5

.github/workflows/iblatlas_ci.yml

@@ -16,12 +16,12 @@ jobs:
       max-parallel: 4
       matrix:
         os: ["windows-latest", "ubuntu-latest"]
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.10", "3.12"]
         exclude:
           - os: windows-latest
-            python-version: 3.8
+            python-version: 3.10
           - os: ubuntu-latest
-            python-version: 3.11
+            python-version: 3.12
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/pypi_publish.yml

@@ -18,7 +18,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.8'
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

CHANGELOG.md

@@ -1,3 +1,8 @@
+## [0.5.5]
+### Modified
+- removed instances of `np.NaN` to replace with `np.nan` for numpy 2.0 compatibility
+- set python 3.10 as minimum python version
+
 ## [0.5.4]
 ### Modified
 - `iblatlas.plots.plot_swanson_vector` option to show colorbar

README.md

@@ -1,6 +1,6 @@
 # iblatlas
 Tools to manipulate hierarchical 3D representations of the mouse brain anatomy for electrophysiolgy experiments.
-The tools are mainly using the the Allen CCF although some other atlases can be used.
+The tools are mainly using the Allen CCF although some other atlases can be used.
 
 **This repository uses minimal requirements, based of standard `matplotlib`, `numpy` and `scipy` libraries, to the exclusion
 of more complex visualization tools such as `pyqt`.**

iblatlas/__init__.py

@@ -194,4 +194,4 @@
 .. [10] Allen Mouse Common Coordinate Framework Technical White Paper (October 2017 v3)
    http://help.brain-map.org/download/attachments/8323525/Mouse_Common_Coordinate_Framework.pdf
 """
-__version__ = '0.5.4'
+__version__ = '0.5.5'

iblatlas/atlas.py

@@ -1493,7 +1493,7 @@ def compute_regions_volume(self, cumsum=False):
             self.regions.volume = self.regions.volume * (self.res_um / 1e3) ** 3
 
 
-def NeedlesAtlas(*args, **kwargs):
+def NeedlesAtlas(*args, **kwargs) -> AllenAtlas:
     """
     Instantiates an atlas.BrainAtlas corresponding to the Allen CCF at the given resolution
     using the IBL Bregma and coordinate system. The Needles atlas defines a stretch along AP

iblatlas/genomics/merfish_scrapping/01_ingest_zhuang.py

@@ -45,7 +45,7 @@ def int_after_colon(text):
         captured_integer = int(match.group(1))
         return float(captured_integer)
     else:
-        return np.NaN
+        return np.nan
 
 
 def fcn_groupby_check_unique(df_cells, group, fields):
@@ -79,7 +79,7 @@ def reindex_missing_rows(df):
         elif isinstance(missing_rec[k], int | np.uint32 | np.int32 | np.uint64 | np.int64):
             missing_rec[k] = 0
         elif isinstance(missing_rec[k], float | np.float32 | np.float64):
-            missing_rec[k] = np.NaN
+            missing_rec[k] = np.nan
     df = df.reindex(pd.Index(np.arange(np.max(df.index) + 1), name=df.index.name), fill_value=0)
     df.iloc[imiss, :] = missing_rec
     return df

iblatlas/plots.py

@@ -831,7 +831,7 @@ def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br
                         annotate_order='top', annotate_list=None, mask=None, mask_color='w', fontsize=10,
                         show_cbar=False, extend='neither', **kwargs):
     """
-    Function to plot scalar value per allen region on the swanson projection. Plots on a vecortised version of the
+    Function to plot scalar value per allen region on the swanson projection. Plots on a vectorised version of the
     swanson projection
 
     Parameters

iblatlas/regions.py

@@ -658,7 +658,7 @@ def propagate_down(self, acronyms, values):
         _, user_indices = ismember(user_aids, self.id)
         self.compute_hierarchy()
         ia, ib = ismember(self.hierarchy, user_indices)
-        v = np.zeros_like(ia, dtype=np.float64) * np.NaN
+        v = np.zeros_like(ia, dtype=np.float64) * np.nan
         v[ia] = values[ib]
         all_values = np.nanmedian(v, axis=0)
         indices = np.where(np.any(ia, axis=0))[0]

iblatlas/tests/test_atlas.py

@@ -42,7 +42,7 @@ def test_rgba(self):
 
     def test_get(self):
         ctx = self.brs.get(688)
-        self.assertTrue(len(ctx.acronym) == 1 and ctx.acronym == 'CTX')
+        self.assertEqual('CTX', ctx.acronym)
 
     def test_ancestors_descendants(self):
         # here we use the same brain region as in the alyx test
@@ -527,7 +527,7 @@ def test_init_from_dict(self):
 
         brain_atlas = _create_mock_atlas()
         brain_atlas.compute_surface()
-        brain_atlas.top = brain_atlas.top * np.NaN
+        brain_atlas.top = brain_atlas.top * np.nan
         ins = Insertion.from_dict(d, brain_atlas=brain_atlas)
         # eval the entry point, should be super close
         dxyz = ins.trajectory.eval_x(d['x'] / 1e6) - np.array((d['x'], d['y'], d['z'])) / 1e6
@@ -562,7 +562,7 @@ def test_init_from_track(self):
         brain_exit = insertion.get_brain_exit(insertion.trajectory, brain_atlas)
         self.assertTrue(brain_exit[2] == brain_atlas.bc.i2z(104))
         # test getting no intersection with the brain surface
-        brain_atlas.srf_xyz *= np.NaN
+        brain_atlas.srf_xyz *= np.nan
         with self.assertRaises(ValueError):
             insertion.get_brain_entry(insertion.trajectory, brain_atlas)
         self.assertIsNone(insertion.get_brain_entry(insertion.trajectory, brain_atlas, mode='none'))

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "iblatlas"
 description = "IBL atlas module"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 license = {file = "LICENSE"}
 authors = [
     {name = "IBL staff", email = "info@internationalbrainlab.org"},