Revert "Add the "decollage" process for raw microscope output to the package"

cyto_ml/tests/conftest.py

@@ -1,5 +1,4 @@
 import os
-import shutil
 import pytest
 from cyto_ml.models.scivision import (
     load_model,
@@ -9,19 +8,13 @@
 
 
 @pytest.fixture
-def fixture_dir():
+def image_dir():
     """
-    Base directory for the test fixtures (images, metadata)
+    Existing directory of images
     """
-    return os.path.join(os.path.abspath(os.path.dirname(__file__)), "../../fixtures/")
-
-
-@pytest.fixture
-def image_dir(fixture_dir):
-    """
-    Directory with single plankton images
-    """
-    return os.path.join(fixture_dir, "test_images")
+    return os.path.join(
+        os.path.abspath(os.path.dirname(__file__)), "fixtures/test_images/"
+    )
 
 
 @pytest.fixture
@@ -50,33 +43,3 @@ def env_endpoint():
     if endpoint and "https" not in endpoint:
         endpoint = None
     return endpoint
-
-
-@pytest.fixture
-def lst_file(fixture_dir):
-    """Location of a metadata file for a FlowCam image batch"""
-    return os.path.join(
-        fixture_dir,
-        "MicrobialMethane_MESO_Tank10_54.0143_-2.7770_04052023_1/metadata.lst",
-    )
-
-
-@pytest.fixture
-def collage_file(fixture_dir):
-    """Location of a collage file with a FlowCam image batch"""
-    return os.path.join(
-        fixture_dir,
-        "MicrobialMethane_MESO_Tank10_54.0143_-2.7770_04052023_1/MicrobialMethane_MESO_Tank10_54.0143_-2.7770_04052023_1_images_000001.tif",  # noqa: E501
-    )  # noqa: E501
-
-
-@pytest.fixture
-def exiftest_file(fixture_dir):
-    """This runs in-place so make a copy of the file every time"""
-    orig = os.path.join(
-        fixture_dir,
-        "MicrobialMethane_MESO_Tank10_54.0143_-2.7770_04052023_1/exiftest.tif",
-    )
-    temp = orig.replace("exiftest", "temp")
-    shutil.copyfile(orig, temp)
-    return temp

environment.yml

@@ -5,7 +5,7 @@ channels:
   - defaults
 dependencies:
   - python=3.9
-  - pytorch=1.10.0  # pinned here for the scivision model
+  - pytorch=1.10.0
   - mkl=2024.0
   - chromadb=0.5.3
   - intake-xarray
@@ -21,6 +21,5 @@ dependencies:
   - streamlit
   - plotly
   - pip:
-    - pyexiftool
     - scivision
     - git+https://github.com/alan-turing-institute/plankton-cefas-scivision@main