rename

CONTRIBUTING.md

@@ -14,7 +14,7 @@ description of the proposed change, including the use case for the change.
 
 ## Contributing to the codebase
 
-To contribute to the codebase, open a pull request on the [Pull Requests](https://github.com/Bayer-Group/phenx/pulls).
+To contribute to the codebase, open a pull request on the [Pull Requests](https://github.com/Bayer-Group/PhenEx/pulls).
 
 All pull requests must be approved by at least one reviewer. If there is a
 dispute regarding a pull request, a second reviewer will be asked to review the

README.md

@@ -1,8 +1,8 @@
 # PhenEx: Automatic PHENotype EXtractor
 
-<a href="https://github.com/Bayer-Group/phenx">
+<a href="https://github.com/Bayer-Group/PhenEx">
   <div style="text-align: center;">
-    <img src="phenx.png" alt="PhenEx Logo" width="500" />
+    <img src="phenex.png" alt="PhenEx Logo" width="500" />
   </div>
 </a>
 

docs/api/phenotypes/codelist_phenotype.md

@@ -1,3 +1,3 @@
 # CodelistPhenotype
 
-::: phenx.phenotypes.codelist_phenotype.CodelistPhenotype
+::: phenex.phenotypes.codelist_phenotype.CodelistPhenotype

docs/api/phenotypes/cohort.md

@@ -1,3 +1,3 @@
 # Cohort
 
-::: phenx.phenotypes.cohort.Cohort
+::: phenex.phenotypes.cohort.Cohort

docs/api/phenotypes/measurement_phenotype.md

@@ -1,3 +1,3 @@
 # MeaurementPhenotype
 
-::: phenx.phenotypes.measurement_phenotype.MeasurementPhenotype
+::: phenex.phenotypes.measurement_phenotype.MeasurementPhenotype

docs/tutorials/phenotypes/CodelistPhenotype_Tutorial.ipynb

@@ -51,7 +51,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.core.tables import Codelist\n",
+    "from phenex.core.tables import Codelist\n",
     "\n",
     "# Create a codelist for Atrial Fibrillation\n",
     "af_codelist = Codelist(\n",
@@ -114,7 +114,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import CodelistPhenotype\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
     "# Ex.1 \n",
     "# which patients had an atrial fibrillation diagnosis at **any time** in the data source?\n",
     "af_phenotype = CodelistPhenotype(\n",
@@ -196,8 +196,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import CodelistPhenotype\n",
-    "from phenx.operations.filters import (\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
+    "from phenex.operations.filters import (\n",
     "    GreaterThanOrEqualTo,\n",
     "    LessThan,\n",
     "    RelativeTimeRangeFilter, \n",
@@ -270,8 +270,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import CodelistPhenotype\n",
-    "from phenx.operations.filters import (\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
+    "from phenex.operations.filters import (\n",
     "    LessThanOrEqualTo,\n",
     "    RelativeTimeRangeFilter\n",
     ")\n",
@@ -336,8 +336,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import CodelistPhenotype\n",
-    "from phenx.operations.filters import (\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
+    "from phenex.operations.filters import (\n",
     "    CategoricalFilter\n",
     ")\n",
     "\n",
@@ -378,8 +378,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import CodelistPhenotype\n",
-    "from phenx.operations.filters import (\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
+    "from phenex.operations.filters import (\n",
     "    CategoricalFilter\n",
     ")\n",
     "\n",
@@ -428,8 +428,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import CodelistPhenotype\n",
-    "from phenx.operations.filters import (\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
+    "from phenex.operations.filters import (\n",
     "    LessThanOrEqualTo,\n",
     "    RelativeTimeRangeFilter, \n",
     "    CategoricalFilter\n",
@@ -498,9 +498,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import CodelistPhenotype\n",
-    "from phenx.phenotypes import CodelistPhenotype\n",
-    "from phenx.operations.filters import (\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
+    "from phenex.phenotypes import CodelistPhenotype\n",
+    "from phenex.operations.filters import (\n",
     "    LessThanOrEqualTo,\n",
     "    RelativeTimeRangeFilter, \n",
     ")\n",

docs/tutorials/phenotypes/MeasurementPhenotype_Tutorial.ipynb

@@ -114,8 +114,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phenx.phenotypes import MeasurementPhenotype\n",
-    "from phenx.core.constants import ONEYEAR_PREINDEX\n",
+    "from phenex.phenotypes import MeasurementPhenotype\n",
+    "from phenex.core.constants import ONEYEAR_PREINDEX\n",
     "# Ex.1 \n",
     "# which patients had a measurement for systolic blood pressure recorded any time in the data source\n",
     "sbp1 = MeasurementPhenotype(\n",

mkdocs.yml

@@ -23,7 +23,7 @@ plugins:
   - mkdocstrings:
       handlers:
         python:
-          paths: [../phenx] # search packages in the src folder
+          paths: [../phenex] # search packages in the src folder
           options:
             docstring_style: "google" # or "numpy", "restructuredtext", etc.
   - mkdocs-jupyter

phenx/filters/codelist_filter.py → phenex/filters/codelist_filter.py

@@ -1,8 +1,8 @@
 import ibis
 
-from phenx.codelists import Codelist
-from phenx.tables import CodeTable, is_phenx_code_table
-from phenx.filters.filter import Filter
+from phenex.codelists import Codelist
+from phenex.tables import CodeTable, is_phenex_code_table
+from phenex.filters.filter import Filter
 from typing import List, Tuple
 import pandas as pd
 
@@ -33,7 +33,7 @@ def _convert_codelist_to_tuples(self) -> List[Tuple[str, str]]:
 
     def _filter(self, code_table: CodeTable) -> CodeTable:
 
-        assert is_phenx_code_table(code_table)
+        assert is_phenex_code_table(code_table)
         input_columns = code_table.columns
 
         # Generate the codelist table as an Ibis literal set

phenx/filters/date_range_filter.py → phenex/filters/date_range_filter.py

@@ -1,7 +1,7 @@
 from typing import Optional
 from datetime import date
 
-from phenx.tables import EventTable, is_phenx_event_table
+from phenex.tables import EventTable, is_phenex_event_table
 
 
 class DateRangeFilter:
@@ -25,7 +25,7 @@ def __init__(
 
     def filter(self, table: EventTable):
 
-        assert is_phenx_event_table(table)
+        assert is_phenex_event_table(table)
 
         conditions = []
         if self.min_date is not None:

phenx/filters/relative_time_range_filter.py → phenex/filters/relative_time_range_filter.py

@@ -1,9 +1,9 @@
 from typing import Optional
 
-# from phenx.phenotypes.phenotype import Phenotype
-from phenx.filters.filter import Filter
-from phenx.tables import EventTable, is_phenx_phenotype_table
-from phenx.filters.value import *
+# from phenex.phenotypes.phenotype import Phenotype
+from phenex.filters.filter import Filter
+from phenex.tables import EventTable, is_phenex_phenotype_table
+from phenex.filters.value import *
 
 
 class RelativeTimeRangeFilter(Filter):

phenx/filters/value.py → phenex/filters/value.py

@@ -1,4 +1,4 @@
-from phenx.filters.filter import Filter
+from phenex.filters.filter import Filter
 
 
 class Value(Filter):

phenx/filters/value_filter.py → phenex/filters/value_filter.py

@@ -1,7 +1,7 @@
 from typing import Optional
-from phenx.filters.filter import Filter
-from phenx.tables import MeasurementTable, is_phenx_phenotype_table
-from phenx.filters.value import *
+from phenex.filters.filter import Filter
+from phenex.tables import MeasurementTable, is_phenex_phenotype_table
+from phenex.filters.value import *
 
 
 class ValueFilter(Filter):

phenx/phenotypes/age_phenotype.py → phenex/phenotypes/age_phenotype.py

@@ -3,10 +3,10 @@
 import ibis
 from ibis.expr.types.relations import Table
 
-from phenx.phenotypes.phenotype import Phenotype
-from phenx.filters.value import Value
-from phenx.tables import PhenotypeTable, is_phenx_person_table
-from phenx.filters.relative_time_range_filter import RelativeTimeRangeFilter
+from phenex.phenotypes.phenotype import Phenotype
+from phenex.filters.value import Value
+from phenex.tables import PhenotypeTable, is_phenex_person_table
+from phenex.filters.relative_time_range_filter import RelativeTimeRangeFilter
 
 
 class AgePhenotype(Phenotype):
@@ -77,7 +77,7 @@ def __init__(
     def _execute(self, tables: Dict[str, Table]) -> PhenotypeTable:
 
         person_table = tables[self.domain]
-        assert is_phenx_person_table(person_table)
+        assert is_phenex_person_table(person_table)
 
         if "YEAR_OF_BIRTH" in person_table.columns:
             date_of_birth = ibis.coalesce(

phenx/phenotypes/codelist_phenotype.py → phenex/phenotypes/codelist_phenotype.py

@@ -1,12 +1,12 @@
 from typing import Union, List
-from phenx.phenotypes.phenotype import Phenotype
-from phenx.filters.codelist_filter import CodelistFilter
-from phenx.filters.relative_time_range_filter import RelativeTimeRangeFilter
-from phenx.filters.date_range_filter import DateRangeFilter
-from phenx.filters.aggregator import First, Last
-from phenx.codelists import Codelist
-from phenx.tables import is_phenx_code_table, PHENOTYPE_TABLE_COLUMNS, PhenotypeTable
-from phenx.phenotypes.functions import select_phenotype_columns
+from phenex.phenotypes.phenotype import Phenotype
+from phenex.filters.codelist_filter import CodelistFilter
+from phenex.filters.relative_time_range_filter import RelativeTimeRangeFilter
+from phenex.filters.date_range_filter import DateRangeFilter
+from phenex.filters.aggregator import First, Last
+from phenex.codelists import Codelist
+from phenex.tables import is_phenex_code_table, PHENOTYPE_TABLE_COLUMNS, PhenotypeTable
+from phenex.phenotypes.functions import select_phenotype_columns
 from ibis import _
 
 
@@ -99,7 +99,7 @@ def _execute(self, tables) -> PhenotypeTable:
         return select_phenotype_columns(code_table)
 
     def _perform_codelist_filtering(self, code_table):
-        assert is_phenx_code_table(code_table)
+        assert is_phenex_code_table(code_table)
         code_table = self.codelist_filter.filter(code_table)
         return code_table
 

phenx/phenotypes/cohort.py → phenex/phenotypes/cohort.py

@@ -1,9 +1,9 @@
 from typing import List, Dict, Optional
-from phenx.phenotypes.phenotype import Phenotype
+from phenex.phenotypes.phenotype import Phenotype
 import ibis
 from ibis.expr.types.relations import Table
-from phenx.tables import PhenotypeTable
-from phenx.phenotypes.functions import hstack
+from phenex.tables import PhenotypeTable
+from phenex.phenotypes.functions import hstack
 
 
 def subset_and_add_index_date(tables: Dict[str, Table], index_table: PhenotypeTable):

phenx/phenotypes/computation_graph.py → phenex/phenotypes/computation_graph.py

@@ -2,7 +2,7 @@
 from datetime import date
 import ibis
 from ibis.expr.types.relations import Table
-from phenx.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
+from phenex.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
 
 
 class ComputationGraph:

phenx/phenotypes/computation_graph_phenotypes.py → phenex/phenotypes/computation_graph_phenotypes.py

@@ -1,9 +1,9 @@
 from typing import Dict, Union
 from ibis.expr.types.relations import Table
 import ibis
-from phenx.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
-from phenx.phenotypes.phenotype import Phenotype, ComputationGraph
-from phenx.phenotypes.functions import hstack
+from phenex.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
+from phenex.phenotypes.phenotype import Phenotype, ComputationGraph
+from phenex.phenotypes.functions import hstack
 from datetime import date
 
 

phenx/phenotypes/logic_phenotype.py → phenex/phenotypes/logic_phenotype.py

@@ -1,7 +1,7 @@
 from typing import Dict, Union
 from ibis.expr.types.relations import Table
-from phenx.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
-from phenx.phenotypes.phenotype import Phenotype
+from phenex.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
+from phenex.phenotypes.phenotype import Phenotype
 
 
 class LogicPhenotype(Phenotype):

phenx/phenotypes/measurement_phenotype.py → phenex/phenotypes/measurement_phenotype.py

@@ -1,7 +1,7 @@
 from typing import Union, List, Optional
-from phenx.phenotypes import CodelistPhenotype
-from phenx.tables import is_phenx_code_table, PHENOTYPE_TABLE_COLUMNS, PhenotypeTable
-from phenx.phenotypes.functions import select_phenotype_columns
+from phenex.phenotypes import CodelistPhenotype
+from phenex.tables import is_phenex_code_table, PHENOTYPE_TABLE_COLUMNS, PhenotypeTable
+from phenex.phenotypes.functions import select_phenotype_columns
 
 from ibis import _
 

phenx/phenotypes/multiple_occurrences_phenotype.py → phenex/phenotypes/multiple_occurrences_phenotype.py

@@ -1,9 +1,9 @@
-from phenx.phenotypes.phenotype import Phenotype
-from phenx.filters.codelist_filter import CodelistFilter
-from phenx.filters.relative_time_range_filter import RelativeTimeRangeFilter
-from phenx.filters.date_range_filter import DateRangeFilter
-from phenx.codelists import Codelist
-from phenx.tables import is_phenx_code_table, PHENOTYPE_TABLE_COLUMNS, PhenotypeTable
+from phenex.phenotypes.phenotype import Phenotype
+from phenex.filters.codelist_filter import CodelistFilter
+from phenex.filters.relative_time_range_filter import RelativeTimeRangeFilter
+from phenex.filters.date_range_filter import DateRangeFilter
+from phenex.codelists import Codelist
+from phenex.tables import is_phenex_code_table, PHENOTYPE_TABLE_COLUMNS, PhenotypeTable
 
 from ibis import _
 

phenx/phenotypes/phenotype.py → phenex/phenotypes/phenotype.py

@@ -1,9 +1,9 @@
 from typing import Dict, Union
 from ibis.expr.types.relations import Table
-from phenx.tables import (
+from phenex.tables import (
     PhenotypeTable,
     PHENOTYPE_TABLE_COLUMNS,
-    is_phenx_phenotype_table,
+    is_phenex_phenotype_table,
 )
 
 
@@ -54,7 +54,7 @@ def execute(self, tables: Dict[str, Table]) -> PhenotypeTable:
             )
 
         self.table = table.select(PHENOTYPE_TABLE_COLUMNS)
-        assert is_phenx_phenotype_table(self.table)
+        assert is_phenex_phenotype_table(self.table)
 
         return self.table
 
@@ -152,7 +152,7 @@ def get_codelists(self, to_pandas=False):
 from datetime import date
 import ibis
 from ibis.expr.types.relations import Table
-from phenx.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
+from phenex.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
 
 
 class ComputationGraph:

phenx/phenotypes/score_phenotype.py → phenex/phenotypes/score_phenotype.py

@@ -1,8 +1,8 @@
 import ast
 from typing import Dict, Union
 from ibis.expr.types.relations import Table
-from phenx.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
-from phenx.phenotypes.phenotype import Phenotype
+from phenex.tables import PhenotypeTable, PHENOTYPE_TABLE_COLUMNS
+from phenex.phenotypes.phenotype import Phenotype
 
 
 class ScorePhenotype(Phenotype):