Merge branch 'release/3.2.0'

dermatologist · Jan 20, 2023 · 483f2b1 · 483f2b1
2 parents b43b394 + 07d5c3c
commit 483f2b1
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Showing 11 changed files with 55 additions and 40 deletions.
diff --git a/.github/workflows/bump.yml b/.github/workflows/bump.yml
@@ -13,7 +13,7 @@ jobs:
 
     steps:
     - name: Checkout Latest Commit
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Generate changelog
       uses: charmixer/auto-changelog-action@v1

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -10,9 +10,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v2.3.4
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2.2.2
+      uses: actions/setup-python@v2.3.1
       with:
         python-version: '3.8'
     - name: Install dependencies
@@ -22,6 +22,7 @@ jobs:
     - name: Create docs
       run: |
         make -C docs/ html
+        cp docs/_config.yml docs/_build/html/_config.yml
     - name: Deploy Docs 🚀
       uses: JamesIves/github-pages-deploy-action@4.1.5
       with:

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -10,9 +10,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 20
     steps:
-    - uses: actions/checkout@v2.3.4
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2.2.2
+      uses: actions/setup-python@v2.3.1
       with:
         python-version: '3.8'
     - name: Install dependencies

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -19,9 +19,9 @@ jobs:
         python-version: [3.7]
 
     steps:
-    - uses: actions/checkout@v2.3.4
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2.2.2
+      uses: actions/setup-python@v2.3.1
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml
@@ -15,9 +15,9 @@ jobs:
         python-version: [3.8]
 
     steps:
-    - uses: actions/checkout@v2.3.4
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2.2.2
+      uses: actions/setup-python@v2.3.1
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,8 @@
 # Changelog
 
-## [Unreleased](https://github.com/dermatologist/pyomop/tree/HEAD)
+## [3.1.0](https://github.com/dermatologist/pyomop/tree/3.1.0) (2021-09-17)
 
-[Full Changelog](https://github.com/dermatologist/pyomop/compare/3.0.0...HEAD)
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/3.0.0...3.1.0)
 
 **Closed issues:**
 

diff --git a/README.md b/README.md
@@ -1,22 +1,32 @@
-# :notebook: pyomop
+# pyomop
 
+![Libraries.io SourceRank](https://img.shields.io/librariesio/sourcerank/pypi/pyomop)
 [![forthebadge made-with-python](http://ForTheBadge.com/images/badges/made-with-python.svg)](https://www.python.org/)
 [![PyPI download total](https://img.shields.io/pypi/dm/pyomop.svg)](https://pypi.python.org/pypi/pyomop/)
 [![Build](https://github.com/dermatologist/pyomop/workflows/Python%20Test/badge.svg)](https://nuchange.ca)
 
 * *Inspired by [@jbadger3's](https://github.com/jbadger3) [inspectomop](https://github.com/jbadger3/inspectomop)*
 
+### [Documentation](https://dermatologist.github.io/pyomop/)
+
 ## Description
 
 The [OHSDI](https://www.ohdsi.org/) OMOP Common Data Model allows for the systematic analysis of healthcare observational databases. This is a python library to use the CDM v6 compliant databases using SQLAlchemy as the ORM. **pyomop** also supports converting query results to a pandas dataframe (see below) for use in machine learning pipelines. See some useful [SQL Queries here.](https://github.com/OHDSI/QueryLibrary)
 
-## Installation
+## Installation (stable)
 
 ```
 pip install pyomop
 
 ```
 
+## Installation (current)
+
+* git clone this repository and:
+```
+pip install -e .
+```
+
 ## Usage
 
 ```
@@ -91,6 +101,8 @@ pip install sqlalchemy==1.3.24
 * SqLite
 * More to follow..
 
+## Give us a star ⭐️
+If you find this project useful, give us a star. It helps others discover the project.
 
 ## Contributors
 

diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -18,7 +18,7 @@ charset-normalizer==2.0.6
     # via requests
 commonmark==0.9.1
     # via recommonmark
-coverage==5.5
+coverage[toml]==5.5
     # via pytest-cov
 distlib==0.3.2
     # via virtualenv
@@ -64,7 +64,7 @@ pytest==6.2.5
     # via
     #   -r dev-requirements.in
     #   pytest-cov
-pytest-cov==2.12.1
+pytest-cov==3.0.0
     # via -r dev-requirements.in
 pytz==2021.1
     # via
@@ -101,18 +101,18 @@ sphinxcontrib-serializinghtml==1.1.5
     # via sphinx
 toml==0.10.2
     # via
+    #   coverage
     #   pytest
-    #   pytest-cov
     #   tox
 tomli==1.2.1
     # via setuptools-scm
-tox==3.24.4
+tox==3.24.5
     # via -r dev-requirements.in
 urllib3==1.26.6
     # via requests
 virtualenv==20.8.0
     # via tox
-wheel==0.37.0
+wheel==0.37.1
     # via -r dev-requirements.in
 
 # The following packages are considered to be unsafe in a requirements file:

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -0,0 +1,2 @@
+theme: jekyll-theme-leap-day
+include: [_sources, _modules, _static]
diff --git a/requirements.txt b/requirements.txt
@@ -4,15 +4,15 @@
 #
 #    pip-compile
 #
-click==8.0.1
+click==8.0.3
     # via pyomop (setup.py)
 inflect==5.3.0
     # via sqlacodegen
-numpy==1.21.2
+numpy==1.21.4
     # via pandas
-pandas==1.3.3
+pandas==1.3.5
     # via pyomop (setup.py)
-psycopg2-binary==2.9.1
+psycopg2-binary==2.9.3
     # via pyomop (setup.py)
 python-dateutil==2.8.2
     # via pandas

diff --git a/src/pyomop/vocabulary.py b/src/pyomop/vocabulary.py
@@ -67,45 +67,45 @@ def set_concept(self, concept_code, vocabulary_id=None):
     def create_vocab(self, folder, sample=10):
         if sample < 1000: # nrows=sample
             try:
-                df = pd.read_csv(folder + '/DRUG_STRENGTH.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/DRUG_STRENGTH.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('drug_strength', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('concept', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_RELATIONSHIP.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_RELATIONSHIP.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('concept_relationship', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_ANCESTOR.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_ANCESTOR.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('concept_ancester', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_SYNONYM.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_SYNONYM.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('concept_synonym', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/VOCABULARY.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/VOCABULARY.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('vocabulary', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/RELATIONSHIP.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/RELATIONSHIP.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('relationship', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_CLASS.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_CLASS.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('concept_class', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/DOMAIN.csv', sep='\t', nrows=sample,  error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/DOMAIN.csv', sep='\t', nrows=sample, on_bad_lines='skip')
                 df.to_sql('domain', con=self._engine, if_exists = 'replace')
             except ValueError:
                 print("Oops!  Could not write vocabulary")
         else:
             try:
-                df = pd.read_csv(folder + '/DRUG_STRENGTH.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/DRUG_STRENGTH.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('drug_strength', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('concept', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_RELATIONSHIP.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_RELATIONSHIP.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('concept_relationship', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_ANCESTOR.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_ANCESTOR.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('concept_ancester', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_SYNONYM.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_SYNONYM.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('concept_synonym', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/VOCABULARY.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/VOCABULARY.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('vocabulary', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/RELATIONSHIP.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/RELATIONSHIP.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('relationship', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/CONCEPT_CLASS.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/CONCEPT_CLASS.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('concept_class', con=self._engine, if_exists = 'replace')
-                df = pd.read_csv(folder + '/DOMAIN.csv', sep='\t', error_bad_lines=False, warn_bad_lines=True)
+                df = pd.read_csv(folder + '/DOMAIN.csv', sep='\t', on_bad_lines='skip')
                 df.to_sql('domain', con=self._engine, if_exists = 'replace')
             except ValueError:
                 print("Oops!  Could not write vocabulary")