Merge pull request #29 from asyml/update_package_name

Update package name to forte.health
asyml · May 31, 2022 · 2db74eb · 2db74eb
2 parents 2b80d30 + d306fe2
commit 2db74eb
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -62,22 +62,22 @@ jobs:
 
     - name: Format check with Black
       run: |
-        black --line-length 80 --check forte_medical/ tests/
+        black --line-length 80 --check fortex/ tests/
 
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 forte_medical/ examples/ tests/ ftx/ --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 fortex/ examples/ tests/ ftx/ --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 forte_medical/ examples/ ftx/ tests/ --ignore E203,W503 --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 fortex/ examples/ ftx/ tests/ --ignore E203,W503 --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
     - name: Lint with pylint
       run: |
-        pylint forte_medical/ tests/
+        pylint fortex/ tests/
 
     - name: Lint main code with mypy when torch version is not 1.5.0 and python is 3.9
       run: |
-        if [[ ${{ matrix.torch-version }} != "1.5.0" && ${{ matrix.python-version }} == "3.9" ]]; then mypy forte_medical/ tests/ ; fi
+        if [[ ${{ matrix.torch-version }} != "1.5.0" && ${{ matrix.python-version }} == "3.9" ]]; then mypy fortex/ tests/ ; fi
 
     - name: Install requirements for tests
       run: |
@@ -92,7 +92,7 @@ jobs:
     - name: Test with pytest and run coverage
       run: |
         coverage run -m pytest tests/
-#        coverage run --append -m pytest --doctest-modules forte_medical/
+#        coverage run --append -m pytest --doctest-modules fortex/
 
     - uses: codecov/codecov-action@v2
       with:

diff --git a/README.md b/README.md
@@ -64,7 +64,7 @@ from forte.data.readers import PlainTextReader
 from forte.pipeline import Pipeline
 from ft.onto.base_ontology import Sentence, EntityMention
 from ftx.medical.clinical_ontology import NegationContext, MedicalEntityMention
-from forte_medical.processors.negation_context_analyzer import (
+from fortex.health.processors.negation_context_analyzer import (
     NegationContextAnalyzer,
 )
 

diff --git a/docs/code/processors.rst b/docs/code/processors.rst
@@ -6,5 +6,5 @@ Processors
 
 :hidden:`NegationContextAnalyzer`
 -------------------------------------
-.. autoclass:: forte_medical.processors.negation_context_analyzer.NegationContextAnalyzer
+.. autoclass:: fortex.health.processors.negation_context_analyzer.NegationContextAnalyzer
     :members:
diff --git a/docs/code/readers.rst b/docs/code/readers.rst
@@ -6,5 +6,5 @@ Readers
 
 :hidden:`Mimic3DischargeNoteReader`
 -------------------------------------
-.. autoclass:: forte_medical.readers.mimic3_note_reader.Mimic3DischargeNoteReader
+.. autoclass:: fortex.health.readers.mimic3_note_reader.Mimic3DischargeNoteReader
     :members:
diff --git a/docs/conf.py b/docs/conf.py
@@ -22,7 +22,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath(".."))
-from forte_medical import __version__
+from fortex.health import __version__
 
 # -- General configuration ------------------------------------------------
 

diff --git a/examples/mimic_iii/medical_pipeline.py b/examples/mimic_iii/medical_pipeline.py
@@ -16,8 +16,8 @@
 )
 from fortex.spacy import SpacyProcessor
 
-from forte_medical.readers.mimic3_note_reader import Mimic3DischargeNoteReader
-from forte_medical.processors.negation_context_analyzer import (
+from fortex.health.readers.mimic3_note_reader import Mimic3DischargeNoteReader
+from fortex.health.processors.negation_context_analyzer import (
     NegationContextAnalyzer,
 )
 

diff --git a/forte_medical/__init__.py → fortex/health/__init__.py b/forte_medical/__init__.py → fortex/health/__init__.py
diff --git a/forte_medical/models/model_base.py → fortex/health/models/model_base.py b/forte_medical/models/model_base.py → fortex/health/models/model_base.py
diff --git a/...cal/ontology_specs/clinical_ontology.json → ...lth/ontology_specs/clinical_ontology.json b/...cal/ontology_specs/clinical_ontology.json → ...lth/ontology_specs/clinical_ontology.json
diff --git a/...edical/processors/icd_coding_processor.py → ...health/processors/icd_coding_processor.py b/...edical/processors/icd_coding_processor.py → ...health/processors/icd_coding_processor.py
@@ -14,7 +14,7 @@
 """
 ICD Coding Processor
 """
-from typing import Dict, List, Set
+from typing import Dict, Set
 import importlib
 
 from transformers import pipeline

diff --git a/...l/processors/negation_context_analyzer.py → ...h/processors/negation_context_analyzer.py b/...l/processors/negation_context_analyzer.py → ...h/processors/negation_context_analyzer.py
diff --git a/forte_medical/readers/__init__.py → fortex/health/readers/__init__.py b/forte_medical/readers/__init__.py → fortex/health/readers/__init__.py
@@ -12,4 +12,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from forte_medical.readers.mimic3_note_reader import *
+from fortex.health.readers.mimic3_note_reader import *
diff --git a/forte_medical/readers/mimic3_note_reader.py → fortex/health/readers/mimic3_note_reader.py b/forte_medical/readers/mimic3_note_reader.py → fortex/health/readers/mimic3_note_reader.py
diff --git a/forte_medical/resources/negex_triggers.txt → fortex/health/resources/negex_triggers.txt b/forte_medical/resources/negex_triggers.txt → fortex/health/resources/negex_triggers.txt