Merge pull request #29 from fractal-analytics-platform/update-depende…

…ncies Update dependencies, drop Python 3.9 support
fractal-analytics-platform · Aug 12, 2024 · 6e2d18f · 6e2d18f
2 parents f3b3401 + 42043f6
commit 6e2d18f
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diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -6,11 +6,11 @@ author_name: Joel Luethi
 git_versioning: true
 github_username: fractal-analytics-platform
 mode: customize
-module_name: fractal_faim_hcs
+module_name: fractal_faim_ipa
 project_license: BSD-3-Clause
-project_name: fractal-faim-hcs
+project_name: fractal-faim-ipa
 project_short_description: Provides Fractal tasks for the MD to OME-Zarr conversion
-    of faim-hcs
+    of faim-ipa
 test_pre_release: false
 use_black: true
 use_mypy: true

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         platform: [ubuntu-latest, macos-latest]
 
     steps:
@@ -54,7 +54,7 @@ jobs:
         run: python -m pip install pytest devtools jsonschema requests wget
 
       - name: 🧪 Run Tests
-        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+        run: pytest -s --color=yes --cov --cov-report=xml --cov-report=term-missing
 
       - name: Coverage
         uses: codecov/codecov-action@v4

diff --git a/README.md b/README.md
@@ -4,7 +4,6 @@
 [![PyPI](https://img.shields.io/pypi/v/fractal-faim-ipa.svg?color=green)](https://pypi.org/project/fractal-faim-ipa)
 [![Python Version](https://img.shields.io/pypi/pyversions/fractal-faim-ipa.svg?color=green)](https://python.org)
 [![CI](https://github.com/jluethi/fractal-faim-ipa/actions/workflows/ci.yml/badge.svg)](https://github.com/jluethi/fractal-faim-ipa/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/jluethi/fractal-faim-ipa/branch/main/graph/badge.svg)](https://codecov.io/gh/jluethi/fractal-faim-ipa)
 
 Provides Fractal tasks for the conversion of Molecular Devices ImageXpress microscope to OME-Zarr.
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -18,7 +18,7 @@ name = "fractal-faim-ipa"
 dynamic = ["version"]
 description = "Provides Fractal tasks for the MD to OME-Zarr conversion of faim-ipa"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "BSD-3-Clause" }
 authors = [
     { name = "Joel Luethi", email = "[email protected]" },
@@ -34,17 +34,17 @@ classifiers = [
 ]
 
 dependencies = [
-    "fractal-tasks-core==1.0.2",
+    "fractal-tasks-core==1.2.1",
     "pydantic",
     "zarr",
-    "faim-ipa==0.3.11",
+    "faim-ipa==0.5.0",
 ]
 
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 # "extras" (e.g. for `pip install .[test]`)
 [project.optional-dependencies]
 # add dependencies used for testing here
-test = ["pytest", "pytest-cov"]
+test = ["pytest", "pytest-cov", "jsonschema"]
 # add anything else you like to have in your dev environment here
 dev = [
     "black",
@@ -53,6 +53,8 @@ dev = [
     "pdbpp",  # https://github.com/pdbpp/pdbpp
     "rich",  # https://github.com/Textualize/rich
     "ruff",
+    "pre-commit",
+    "devtools",
 ]
 
 [project.urls]
@@ -78,8 +80,6 @@ extend-select = [
     "F",    # flakes
     "D",    # pydocstyle
     "I",    # isort
-    "U",    # pyupgrade
-    # "S",    # bandit
     "C",    # flake8-comprehensions
     "B",    # flake8-bugbear
     "A001", # flake8-builtins

diff --git a/src/fractal_faim_ipa/convert_ome_zarr.py b/src/fractal_faim_ipa/convert_ome_zarr.py
@@ -9,15 +9,15 @@
 from faim_ipa.hcs.converter import ConvertToNGFFPlate, NGFFPlate, PlateLayout
 from faim_ipa.stitching import stitching_utils
 from fractal_tasks_core.tables import write_table
-from pydantic.decorator import validate_arguments
+from pydantic import validate_call
 
 from fractal_faim_ipa.md_converter_utils import ModeEnum
 from fractal_faim_ipa.roi_tables import create_ROI_tables
 
 logger = logging.getLogger(__name__)
 
 
-@validate_arguments
+@validate_call
 def convert_ome_zarr(
     *,
     zarr_urls: list[str],

diff --git a/src/fractal_faim_ipa/imagexpress_zmb/ImageXpressPlateAcquisition.py b/src/fractal_faim_ipa/imagexpress_zmb/ImageXpressPlateAcquisition.py
@@ -5,19 +5,19 @@
 from typing import Optional, Union
 
 import pandas as pd
-from tqdm import tqdm
-
 from faim_ipa.hcs.acquisition import (
     PlateAcquisition,
     TileAlignmentOptions,
     WellAcquisition,
 )
+from faim_ipa.io.metadata import ChannelMetadata
+from faim_ipa.io.metaseries import load_metaseries_tiff_metadata
+from faim_ipa.utils import rgb_to_hex, wavelength_to_rgb
+from tqdm import tqdm
+
 from fractal_faim_ipa.imagexpress_zmb.ImageXpressWellAcquisition import (
     ImageXpressWellAcquisition,
 )
-from faim_ipa.io.ChannelMetadata import ChannelMetadata
-from faim_ipa.io.MetaSeriesTiff import load_metaseries_tiff_metadata
-from faim_ipa.utils import rgb_to_hex, wavelength_to_rgb
 
 
 class ImageXpressPlateAcquisition(PlateAcquisition):
@@ -45,8 +45,7 @@ def _parse_files(self) -> pd.DataFrame:
         DataFrame
             Table of all files in the acquisition.
         """
-
-        files =  pd.DataFrame(
+        files = pd.DataFrame(
             ImageXpressPlateAcquisition._list_and_match_files(
                 root_dir=self._acquisition_dir,
                 root_re=self._get_root_re(),

diff --git a/src/fractal_faim_ipa/imagexpress_zmb/ImageXpressWellAcquisition.py b/src/fractal_faim_ipa/imagexpress_zmb/ImageXpressWellAcquisition.py
@@ -1,15 +1,13 @@
 from pathlib import Path
 from typing import Optional, Union
 
-import numpy as np
 import dask
 import dask.array as da
+import numpy as np
 import pandas as pd
-
 from faim_ipa.hcs.acquisition import TileAlignmentOptions, WellAcquisition
-from faim_ipa.io.MetaSeriesTiff import load_metaseries_tiff_metadata
-from faim_ipa.stitching import Tile
-from faim_ipa.stitching.Tile import TilePosition
+from faim_ipa.io.metaseries import load_metaseries_tiff_metadata
+from faim_ipa.stitching.tile import Tile, TilePosition
 
 
 class ImageXpressWellAcquisition(WellAcquisition):
@@ -32,28 +30,30 @@ def __init__(
     def _assemble_tiles(self) -> list[Tile]:
         def _load_positions(fn):
             metadata = load_metaseries_tiff_metadata(fn)
-            out = np.array([
-                metadata["pixel-size-y"],
-                metadata["pixel-size-x"],
-                int(metadata["stage-position-y"] / metadata["spatial-calibration-y"]),
-                int(metadata["stage-position-x"] / metadata["spatial-calibration-x"]),
-            ])
+            out = np.array(
+                [
+                    metadata["pixel-size-y"],
+                    metadata["pixel-size-x"],
+                    int(
+                        metadata["stage-position-y"] / metadata["spatial-calibration-y"]
+                    ),
+                    int(
+                        metadata["stage-position-x"] / metadata["spatial-calibration-x"]
+                    ),
+                ]
+            )
             return out
-        
+
         fns = self._files.path.to_numpy()
         lazy_positions = [dask.delayed(_load_positions)(fn) for fn in fns]
         arrays = [
-            da.from_delayed(
-                lazy_position,
-                dtype=int,
-                shape=(4,)
-            )
+            da.from_delayed(lazy_position, dtype=int, shape=(4,))
             for lazy_position in lazy_positions
         ]
         positions = da.stack(arrays, axis=0).compute()
 
         tiles = []
-        for (i, row), pos in zip(self._files.iterrows(), positions):
+        for (_i, row), pos in zip(self._files.iterrows(), positions):
             file = row["path"]
             time_point = row["t"] if "t" in row.index and row["t"] is not None else 0
             channel = row["channel"]
@@ -98,12 +98,12 @@ def get_axes(self) -> list[str]:
         axes = ["y", "x"]
 
         if "z" in self._files.columns:
-            axes = ["z"] + axes
+            axes = ["z", *axes]
 
         if self._files["channel"].nunique() > 1:
-            axes = ["c"] + axes
+            axes = ["c", *axes]
 
         if "t" in self._files.columns and self._files["t"].nunique() > 1:
-            axes = ["t"] + axes
+            axes = ["t", *axes]
 
         return axes
diff --git a/src/fractal_faim_ipa/imagexpress_zmb/MixedAcquisition.py b/src/fractal_faim_ipa/imagexpress_zmb/MixedAcquisition.py
@@ -5,10 +5,10 @@
 
 import numpy as np
 import pandas as pd
-
 from faim_ipa.hcs.acquisition import TileAlignmentOptions
+from faim_ipa.io.metaseries import load_metaseries_tiff_metadata
+
 from fractal_faim_ipa.imagexpress_zmb import ImageXpressPlateAcquisition
-from faim_ipa.io.MetaSeriesTiff import load_metaseries_tiff_metadata
 
 
 class MixedAcquisition(ImageXpressPlateAcquisition):
@@ -19,14 +19,14 @@ class MixedAcquisition(ImageXpressPlateAcquisition):
     └── 2023-02-21 --> {date}
         └── 1334 --> {acquisition id}
             ├── ZStep_1
-            │   ├── Projection-Mix_E07_s1_w1E78EB128-BD0D-4D94-A6AD-3FF28BB1B105.tif
-            │   ├── Projection-Mix_E07_s1_w1_thumb187DE64B-038A-4671-BF6B-683721723769.tif
-            │   ├── Projection-Mix_E07_s1_w2C0A49256-E289-4C0F-ADC9-F7728ABDB141.tif
-            │   ├── Projection-Mix_E07_s1_w2_thumb57D4B151-71BF-480E-8CC4-C23A2690B763.tif
-            │   ├── Projection-Mix_E07_s1_w427CCB2E4-1BF4-45E7-8BC7-264B48EF9C4A.tif
-            │   ├── Projection-Mix_E07_s1_w4_thumb555647D0-77F1-4A43-9472-AE509F95E236.tif
-            │   ├── ...
-            │   └── Projection-Mix_E08_s2_w4_thumbD2785594-4F49-464F-9F80-1B82E30A560A.tif
+            │   ├── Projection-Mix_E07_s1_w1E78EB128-BD0D-4D94-A6AD-3FF28BB1B105.tif
+            │   ├── Projection-Mix_E07_s1_w1_thumb187DE64B-038A-4671-BF6B-683721723769.tif
+            │   ├── Projection-Mix_E07_s1_w2C0A49256-E289-4C0F-ADC9-F7728ABDB141.tif
+            │   ├── Projection-Mix_E07_s1_w2_thumb57D4B151-71BF-480E-8CC4-C23A2690B763.tif
+            │   ├── Projection-Mix_E07_s1_w427CCB2E4-1BF4-45E7-8BC7-264B48EF9C4A.tif
+            │   ├── Projection-Mix_E07_s1_w4_thumb555647D0-77F1-4A43-9472-AE509F95E236.tif
+            │   ├── ...
+            │   └── Projection-Mix_E08_s2_w4_thumbD2785594-4F49-464F-9F80-1B82E30A560A.tif
             ├── ...
             └── ZStep_9
                 ├── Projection-Mix_E07_s1_w1091EB8A5-272A-466D-B8A0-7547C6BA392B.tif
@@ -60,7 +60,9 @@ def _parse_files(self) -> pd.DataFrame:
         # single-planes and projections are unnecessarily duplicated
         # -> remove duplicates from files
         for c in files.channel.unique():
-            file = files[(files.channel == c) & (files.z!='0') & (files.z!='1')].iloc[0]
+            file = files[
+                (files.channel == c) & (files.z != "0") & (files.z != "1")
+            ].iloc[0]
             metadata = load_metaseries_tiff_metadata(file.path)
             # projections have no "Z Step" attribute
             # single-planes have always metadata["Z Step"] == 1, for each duplicate
@@ -73,9 +75,7 @@ def _parse_files(self) -> pd.DataFrame:
         return files
 
     def _get_root_re(self) -> re.Pattern:
-        return re.compile(
-            r".*[\/\\]TimePoint_(?P<t>\d+)[\/\\]ZStep_(?!0)(?P<z>\d+)"
-        )
+        return re.compile(r".*[\/\\]TimePoint_(?P<t>\d+)[\/\\]ZStep_(?!0)(?P<z>\d+)")
 
     def _get_filename_re(self) -> re.Pattern:
         return re.compile(
@@ -87,14 +87,14 @@ def _get_z_spacing(self) -> Optional[float]:
 
     def _compute_z_spacing(self, files: pd.DataFrame) -> Optional[float]:
         assert "z" in files.columns, "No z column in files DataFrame."
-        channel_with_stack = np.sort(files[files.z!='1']["channel"].unique())[0]
+        channel_with_stack = np.sort(files[files.z != "1"]["channel"].unique())[0]
         subset = files[files["channel"] == channel_with_stack]
         subset = subset[subset["well"] == np.sort(subset["well"].unique())[0]]
         subset = subset[subset["field"] == np.sort(subset["field"].unique())[0]]
 
         plane_positions = []
 
-        for i, row in subset.iterrows():
+        for _i, row in subset.iterrows():
             file = row["path"]
             if "z" in row.keys() and row["z"] is not None:
                 metadata = load_metaseries_tiff_metadata(file)

diff --git a/src/fractal_faim_ipa/imagexpress_zmb/StackAcquisition.py b/src/fractal_faim_ipa/imagexpress_zmb/StackAcquisition.py
@@ -5,10 +5,10 @@
 
 import numpy as np
 import pandas as pd
-
 from faim_ipa.hcs.acquisition import TileAlignmentOptions
+from faim_ipa.io.metaseries import load_metaseries_tiff_metadata
+
 from fractal_faim_ipa.imagexpress_zmb import ImageXpressPlateAcquisition
-from faim_ipa.io.MetaSeriesTiff import load_metaseries_tiff_metadata
 
 
 class StackAcquisition(ImageXpressPlateAcquisition):
@@ -19,14 +19,14 @@ class StackAcquisition(ImageXpressPlateAcquisition):
     └── 2023-02-21 --> {date}
         └── 1334 --> {acquisition id}
             ├── ZStep_1
-            │   ├── Projection-Mix_E07_s1_w1E78EB128-BD0D-4D94-A6AD-3FF28BB1B105.tif
-            │   ├── Projection-Mix_E07_s1_w1_thumb187DE64B-038A-4671-BF6B-683721723769.tif
-            │   ├── Projection-Mix_E07_s1_w2C0A49256-E289-4C0F-ADC9-F7728ABDB141.tif
-            │   ├── Projection-Mix_E07_s1_w2_thumb57D4B151-71BF-480E-8CC4-C23A2690B763.tif
-            │   ├── Projection-Mix_E07_s1_w427CCB2E4-1BF4-45E7-8BC7-264B48EF9C4A.tif
-            │   ├── Projection-Mix_E07_s1_w4_thumb555647D0-77F1-4A43-9472-AE509F95E236.tif
-            │   ├── ...
-            │   └── Projection-Mix_E08_s2_w4_thumbD2785594-4F49-464F-9F80-1B82E30A560A.tif
+            │   ├── Projection-Mix_E07_s1_w1E78EB128-BD0D-4D94-A6AD-3FF28BB1B105.tif
+            │   ├── Projection-Mix_E07_s1_w1_thumb187DE64B-038A-4671-BF6B-683721723769.tif
+            │   ├── Projection-Mix_E07_s1_w2C0A49256-E289-4C0F-ADC9-F7728ABDB141.tif
+            │   ├── Projection-Mix_E07_s1_w2_thumb57D4B151-71BF-480E-8CC4-C23A2690B763.tif
+            │   ├── Projection-Mix_E07_s1_w427CCB2E4-1BF4-45E7-8BC7-264B48EF9C4A.tif
+            │   ├── Projection-Mix_E07_s1_w4_thumb555647D0-77F1-4A43-9472-AE509F95E236.tif
+            │   ├── ...
+            │   └── Projection-Mix_E08_s2_w4_thumbD2785594-4F49-464F-9F80-1B82E30A560A.tif
             ├── ...
             └── ZStep_9
                 ├── Projection-Mix_E07_s1_w1091EB8A5-272A-466D-B8A0-7547C6BA392B.tif
@@ -61,7 +61,9 @@ def _parse_files(self) -> pd.DataFrame:
         # single-planes and projections are unnecessarily duplicated
         # -> remove duplicates from files & remove all projections
         for c in files.channel.unique():
-            file = files[(files.channel == c) & (files.z!='0') & (files.z!='1')].iloc[0]
+            file = files[
+                (files.channel == c) & (files.z != "0") & (files.z != "1")
+            ].iloc[0]
             metadata = load_metaseries_tiff_metadata(file.path)
             # projections have no "Z Step" attribute
             # single-planes have always metadata["Z Step"] == 1, for each duplicate
@@ -74,9 +76,7 @@ def _parse_files(self) -> pd.DataFrame:
         return files
 
     def _get_root_re(self) -> re.Pattern:
-        return re.compile(
-            r".*[\/\\]TimePoint_(?P<t>\d+)[\/\\]ZStep_(?!0)(?P<z>\d+)"
-        )
+        return re.compile(r".*[\/\\]TimePoint_(?P<t>\d+)[\/\\]ZStep_(?!0)(?P<z>\d+)")
 
     def _get_filename_re(self) -> re.Pattern:
         return re.compile(
@@ -88,14 +88,14 @@ def _get_z_spacing(self) -> Optional[float]:
 
     def _compute_z_spacing(self, files: pd.DataFrame) -> Optional[float]:
         assert "z" in files.columns, "No z column in files DataFrame."
-        channel_with_stack = np.sort(files[files.z!='1']["channel"].unique())[0]
+        channel_with_stack = np.sort(files[files.z != "1"]["channel"].unique())[0]
         subset = files[files["channel"] == channel_with_stack]
         subset = subset[subset["well"] == np.sort(subset["well"].unique())[0]]
         subset = subset[subset["field"] == np.sort(subset["field"].unique())[0]]
 
         plane_positions = []
 
-        for i, row in subset.iterrows():
+        for _i, row in subset.iterrows():
             file = row["path"]
             if "z" in row.keys() and row["z"] is not None:
                 metadata = load_metaseries_tiff_metadata(file)

diff --git a/src/fractal_faim_ipa/roi_tables.py b/src/fractal_faim_ipa/roi_tables.py
@@ -4,7 +4,7 @@
 import numpy as np
 import pandas as pd
 from faim_ipa.hcs.acquisition import PlateAcquisition, WellAcquisition
-from faim_ipa.stitching import Tile
+from faim_ipa.stitching.tile import Tile
 
 
 def create_ROI_tables(plate_acquisition: PlateAcquisition):