API: Make iamsystem an optional dependency

docs/cookbook/iamsystem.md

@@ -1,10 +1,14 @@
 # IAMSystem Matcher
 
-+++
+This section showcases an example using the IAMSystem matcher.
 
-This tutorial will show an example of iamsystem matcher operation usage.
+:::{note}
+This section requires optional dependencies, use the following to install them:
 
-+++
+```console
+pip install 'medkit-lib[iamsystem-matcher]'
+```
+:::
 
 ## Loading a text document
 

medkit/text/ner/__init__.py

@@ -9,8 +9,6 @@
     "SimstringMatcherRule",
     "SimstringMatcherNormalization",
     "UMLSMatcher",
-    "IAMSystemMatcher",
-    "MedkitKeyword",
     "DateAttribute",
     "DurationAttribute",
     "RelativeDateAttribute",
@@ -26,12 +24,15 @@
     RelativeDateDirection,
 )
 from medkit.text.ner.duckling_matcher import DucklingMatcher
-from medkit.text.ner.iamsystem_matcher import IAMSystemMatcher, MedkitKeyword
 from medkit.text.ner.regexp_matcher import RegexpMatcher, RegexpMatcherNormalization, RegexpMatcherRule, RegexpMetadata
 from medkit.text.ner.simstring_matcher import SimstringMatcher, SimstringMatcherNormalization, SimstringMatcherRule
 from medkit.text.ner.umls_matcher import UMLSMatcher
 
-# quick_umls module
+# iamsystem matcher
+if modules_are_available(["iamsystem"]):
+    __all__ += ["iamsystem_matcher"]
+
+# quickumls matcher
 if modules_are_available(["packaging", "quickumls"]):
     __all__ += ["quick_umls_matcher"]
 

pyproject.toml

@@ -42,7 +42,6 @@ dependencies = [
   "anyascii",
   "duptextfinder>=0.3.0",
   "flashtext>=2.7",
-  "iamsystem>=0.6.0",
   "intervaltree",
   "numpy",
   "pyaml",
@@ -75,6 +74,9 @@ hf-translator = [
 hf-utils = [
   "transformers>=4.21",
 ]
+iamsystem-matcher = [
+  "iamsystem>=0.6.0",
+]
 metrics-diarization = [
   "pyannote-core>=5.0",
   "pyannote-metrics>=3.2.0",
@@ -143,6 +145,7 @@ all = [
     hf-transcriber,\
     hf-translator,\
     hf-utils,\
+    iamsystem-matcher,\
     metrics-diarization,\
     metrics-text-classification,\
     metrics-ner,metrics-transcription,\

tests/conftest.py

@@ -1,7 +1,3 @@
-# must import iamsystem first
-# workaround for failed test quickumls when importing torchaudio,
-# iamsystem then quickumls
-import iamsystem  # noqa:F401
 import pytest
 
 from medkit.core.store import GlobalStore

tests/unit/text/ner/test_iamsystem_matcher.py

@@ -1,3 +1,7 @@
+import pytest
+
+pytest.importorskip(modname="iamsystem", reason="iamsystem is not installed")
+
 from iamsystem import Entity as Term
 from iamsystem import Matcher