Packages not on conda-forge are now optional dependencies (#11)

* Make morphapi and cellfinder optional, adjust tests

* Add optional dependencies to readme

* Tidy up submdule presence tests

* Revert "Tidy up submdule presence tests"

This reverts commit 43a95dd.

* Adjust tests to make mypy happy

* pass is not a test, but import module is

README.md

@@ -28,9 +28,17 @@ The BrainGlobe project is only possible due to grant funding and the generous su
 ## Installation
 
 The `brainglobe` package can be installed from [PyPI](https://pypi.org/project/brainglobe/) into a Python environment by running
-```python
+```sh
 pip install brainglobe
 ```
+
+If you want to install the additional packages `morphapi` and `cellfinder`, you can specify them as optional dependencies:
+```sh
+pip install brainglobe[morphapi] # Include morphapi
+pip install brainglobe[cellfinder] # Include cellfinder
+pip install brainglobe[morphapi,cellfinder] # Include both morphapi and cellfinder
+```
+
 Alternatively, you can download the source from [PyPI here](https://pypi.org/project/brainglobe/#files).
 
 ## Contributing

brainglobe/__init__.py

@@ -12,4 +12,18 @@
 import brainreg
 import brainreg_segment
 import cellfinder_core
-import morphapi
+
+# Determine if optional dependencies were installed,
+# and expose if necessary.
+# morphapi
+_MORPHAPI_INSTALLED = True
+try:
+    import morphapi
+except ImportError:
+    _MORPHAPI_INSTALLED = False
+# cellfinder - not exposed, but still check
+_CELLFINDER_INSTALLED = True
+try:
+    import cellfinder
+except ImportError:
+    _CELLFINDER_INSTALLED = False

pyproject.toml

@@ -30,12 +30,10 @@ dependencies = [
   # "bg-atlasgen", [WIP]
   # "brainglobe-napari", [WIP]
   "brainglobe-napari-io",
-  "morphapi>=0.1.3.0",
   "cellfinder-napari",
   "brainreg-segment>=0.0.2",
   "brainreg",
-  "brainreg-napari",
-  "cellfinder"
+  "brainreg-napari"
 ]
 
 [project.optional-dependencies]
@@ -50,6 +48,12 @@ dev = [
   "ruff",
   "setuptools_scm",
 ]
+morphapi = [
+  "morphapi>=0.1.3.0"
+]
+cellfinder = [
+  "cellfinder"
+]
 
 [build-system]
 requires = [

tests/test_unit/test_tool_exposure.py

@@ -9,8 +9,8 @@
     "brainreg",
     "brainreg_segment",
     "cellfinder_core",
-    "morphapi",
 ]
+OPTIONAL_TOOLS = ["morphapi", "cellfinder"]
 
 
 def test_tool_exposure() -> None:
@@ -23,3 +23,23 @@ def test_tool_exposure() -> None:
         assert inspect.ismodule(
             getattr(bg, exposed_tool)
         ), f"brainglobe.{exposed_tool} is not a submodule"
+
+    # Determine if optional dependencies were installed,
+    # and exposed if necessary
+
+    # morphapi - should be exposed if installed
+    if bg._MORPHAPI_INSTALLED:
+        assert hasattr(
+            bg, "morphapi"
+        ), "morphapi is installed but not exposed."
+        assert inspect.ismodule(
+            bg.morphapi
+        ), "brainglobe.morphapi is not a module"
+    else:
+        assert not hasattr(bg, "morphapi")
+
+    # cellfinder - should not be exposed if installed
+    if bg._CELLFINDER_INSTALLED:
+        assert not hasattr(
+            bg, "cellfinder"
+        ), "brainglobe.cellfinder is exposed"