Merge remote-tracking branch 'upstream/dev' into ci/testing-env

Author: Zeroto521

.github/workflows/docs-preview.yml

@@ -22,14 +22,19 @@ jobs:
         with:
           auto-update-conda: true
           miniforge-variant: Mambaforge
-          environment-file: mkdocs/environment.yaml
+          environment-file: environment-dev.yml
           use-mamba: true
 
       - name: Build docs
         run: |
           pip install .
           mkdocs build
 
+      - uses: actions/upload-artifact@v3
+        with:
+          name: website
+          path: site/
+
       - name: Deploy docs preview to Netlify
         uses: nwtgck/[email protected]
         with:

.requirements/all.txt

@@ -15,9 +15,9 @@ attrs==21.4.0
 backcall==0.2.0
     # via ipython
 biopython==1.79
-    # via -r .requirements/biology.in
+    # via -r biology.in
 black==22.1.0
-    # via -r .requirements/dev.in
+    # via -r dev.in
 cfgv==3.3.1
     # via pre-commit
 click==8.0.4
@@ -31,7 +31,7 @@ colorama==0.4.4
 coverage[toml]==6.3.2
     # via pytest-cov
 darglint==1.8.1
-    # via -r .requirements/dev.in
+    # via -r dev.in
 decorator==5.1.1
     # via ipython
 distlib==0.3.4
@@ -44,26 +44,24 @@ filelock==3.6.0
     # via virtualenv
 flake8==4.0.1
     # via
-    #   -r .requirements/dev.in
+    #   -r dev.in
     #   pandas-vet
 ghp-import==2.0.2
     # via mkdocs
 hypothesis==6.39.3
-    # via -r .requirements/testing.in
+    # via -r testing.in
 identify==2.4.11
     # via pre-commit
 importlib-metadata==4.11.2
-    # via
-    #   markdown
-    #   mkdocs
+    # via mkdocs
 iniconfig==1.1.1
     # via pytest
 interrogate==1.5.0
-    # via -r .requirements/testing.in
+    # via -r testing.in
 ipython==8.1.1
-    # via -r .requirements/docs.in
+    # via -r docs.in
 isort==5.10.1
-    # via -r .requirements/dev.in
+    # via -r dev.in
 jedi==0.18.1
     # via ipython
 jinja2==3.0.3
@@ -90,26 +88,26 @@ mergedeep==1.3.4
     # via mkdocs
 mkdocs==1.2.3
     # via
-    #   -r .requirements/docs.in
+    #   -r docs.in
     #   mkdocs-autorefs
     #   mkdocs-material
     #   mkdocstrings
 mkdocs-autorefs==0.4.1
     # via mkdocstrings
 mkdocs-material==8.2.5
-    # via -r .requirements/docs.in
+    # via -r docs.in
 mkdocs-material-extensions==1.0.3
     # via mkdocs-material
 mkdocstrings==0.17.0
-    # via -r .requirements/docs.in
+    # via -r docs.in
 mpmath==1.2.1
     # via sympy
 multipledispatch==0.6.0
-    # via -r .requirements/base.in
+    # via -r base.in
 mypy-extensions==0.4.3
     # via black
 natsort==8.1.0
-    # via -r .requirements/base.in
+    # via -r base.in
 nodeenv==1.6.0
     # via pre-commit
 numpy==1.22.3
@@ -129,9 +127,9 @@ pandas==1.4.1
     #   pandas-flavor
     #   xarray
 pandas-flavor==0.2.0
-    # via -r .requirements/base.in
+    # via -r base.in
 pandas-vet==0.2.3
-    # via -r .requirements/testing.in
+    # via -r testing.in
 parso==0.8.3
     # via jedi
 pathspec==0.9.0
@@ -143,15 +141,15 @@ pexpect==4.8.0
 pickleshare==0.7.5
     # via ipython
 pip-tools==6.5.1
-    # via -r .requirements/dev.in
+    # via -r dev.in
 platformdirs==2.5.1
     # via
     #   black
     #   virtualenv
 pluggy==1.0.0
     # via pytest
 pre-commit==2.17.0
-    # via -r .requirements/dev.in
+    # via -r dev.in
 prompt-toolkit==3.0.28
     # via ipython
 ptyprocess==0.7.0
@@ -160,11 +158,11 @@ pure-eval==0.2.2
     # via stack-data
 py==1.11.0
     # via
-    #   -r .requirements/testing.in
+    #   -r testing.in
     #   interrogate
     #   pytest
     #   pytest-forked
-py4j==0.10.9.3
+py4j==0.10.9.5
     # via pyspark
 pycodestyle==2.8.0
     # via flake8
@@ -180,20 +178,20 @@ pymdown-extensions==9.2
     #   mkdocstrings
 pyparsing==3.0.7
     # via packaging
-pyspark==3.2.1
-    # via -r .requirements/spark.in
+pyspark==3.2.2
+    # via -r spark.in
 pytest==7.0.1
     # via
-    #   -r .requirements/testing.in
+    #   -r testing.in
     #   pytest-cov
     #   pytest-forked
     #   pytest-xdist
 pytest-cov==3.0.0
-    # via -r .requirements/testing.in
+    # via -r testing.in
 pytest-forked==1.4.0
     # via pytest-xdist
 pytest-xdist==2.5.0
-    # via -r .requirements/testing.in
+    # via -r testing.in
 python-dateutil==2.8.2
     # via
     #   ghp-import
@@ -210,7 +208,7 @@ pyyaml==6.0
 pyyaml-env-tag==0.1
     # via mkdocs
 scipy==1.8.0
-    # via -r .requirements/base.in
+    # via -r base.in
 six==1.16.0
     # via
     #   asttokens
@@ -236,15 +234,13 @@ tomli==2.0.1
     #   pep517
     #   pytest
 tqdm==4.63.0
-    # via -r .requirements/chemistry.in
+    # via -r chemistry.in
 traitlets==5.1.1
     # via
     #   ipython
     #   matplotlib-inline
-typing-extensions==4.1.1
-    # via black
 unyt==2.8.0
-    # via -r .requirements/engineering.in
+    # via -r engineering.in
 virtualenv==20.13.3
     # via pre-commit
 watchdog==2.1.6

.requirements/docs.txt

@@ -9,7 +9,7 @@ asttokens==2.0.5
 backcall==0.2.0
     # via ipython
 biopython==1.79
-    # via -r .requirements/biology.in
+    # via -r biology.in
 click==8.0.4
     # via mkdocs
 decorator==5.1.1
@@ -19,11 +19,9 @@ executing==0.8.3
 ghp-import==2.0.2
     # via mkdocs
 importlib-metadata==4.11.2
-    # via
-    #   markdown
-    #   mkdocs
+    # via mkdocs
 ipython==8.1.1
-    # via -r .requirements/docs.in
+    # via -r docs.in
 jedi==0.18.1
     # via ipython
 jinja2==3.0.3
@@ -48,18 +46,18 @@ mergedeep==1.3.4
     # via mkdocs
 mkdocs==1.2.3
     # via
-    #   -r .requirements/docs.in
+    #   -r docs.in
     #   mkdocs-autorefs
     #   mkdocs-material
     #   mkdocstrings
 mkdocs-autorefs==0.4.1
     # via mkdocstrings
 mkdocs-material==8.2.5
-    # via -r .requirements/docs.in
+    # via -r docs.in
 mkdocs-material-extensions==1.0.3
     # via mkdocs-material
 mkdocstrings==0.17.0
-    # via -r .requirements/docs.in
+    # via -r docs.in
 mpmath==1.2.1
     # via sympy
 numpy==1.22.3
@@ -80,7 +78,7 @@ ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.2
     # via stack-data
-py4j==0.10.9.3
+py4j==0.10.9.5
     # via pyspark
 pygments==2.11.2
     # via
@@ -92,8 +90,8 @@ pymdown-extensions==9.2
     #   mkdocstrings
 pyparsing==3.0.7
     # via packaging
-pyspark==3.2.1
-    # via -r .requirements/spark.in
+pyspark==3.2.2
+    # via -r spark.in
 python-dateutil==2.8.2
     # via ghp-import
 pytkdocs==0.16.1
@@ -113,13 +111,13 @@ stack-data==0.2.0
 sympy==1.10
     # via unyt
 tqdm==4.63.0
-    # via -r .requirements/chemistry.in
+    # via -r chemistry.in
 traitlets==5.1.1
     # via
     #   ipython
     #   matplotlib-inline
 unyt==2.8.0
-    # via -r .requirements/engineering.in
+    # via -r engineering.in
 watchdog==2.1.6
     # via mkdocs
 wcwidth==0.2.5

.requirements/spark.txt

@@ -4,7 +4,7 @@
 #
 #    pip-compile .requirements/spark.in
 #
-py4j==0.10.9.3
+py4j==0.10.9.5
     # via pyspark
-pyspark==3.2.1
-    # via -r .requirements/spark.in
+pyspark==3.2.2
+    # via -r spark.in

CHANGELOG.md

@@ -17,6 +17,8 @@
 -   [INF] Update `mkdocstrings` version and to fit its new coming features. PR #1138 @Zeroto521
 -   [BUG] Force `math.softmax` returning `Series`. PR #1139 @Zeroto521
 -   [INF] Set independent environment for building documentation. PR #1141 @Zeroto521
+-   [DOC] Add local documentation preview via github action artifact. PR #1149 @Zeroto521
+-   [ENH] Enabel `encode_categorical` handle 2 (or more ) dimensions array. PR #1153 @Zeroto521
 
 ## [v0.23.1] - 2022-05-03
 

environment-dev.yml

@@ -22,7 +22,8 @@ dependencies:
   - make
   - mkdocs
   - mkdocs-material
-  - mkdocstrings-python
+  - mkdocstrings=0.18.1
+  - mkdocstrings-python-legacy=0.2.2
   - missingno
   - multipledispatch
   - mypy

janitor/biology.py

@@ -41,32 +41,32 @@ def join_fasta(
 
     Method chaining usage example:
 
-    >>> import tempfile
-    >>> import pandas as pd
-    >>> import janitor.biology
-
-    >>> tf = tempfile.NamedTemporaryFile()
-    >>> tf.write('''>SEQUENCE_1
-    ... MTEITAAMVKELRESTGAGMMDCK
-    ... >SEQUENCE_2
-    ... SATVSEINSETDFVAKN'''.encode('utf8'))
-    66
-    >>> tf.seek(0)
-    0
-
-    >>> df = pd.DataFrame({"sequence_accession":
-    ... ["SEQUENCE_1", "SEQUENCE_2", ]})
-
-    >>> df = df.join_fasta(
-    ...     filename=tf.name,
-    ...     id_col='sequence_accession',
-    ...     column_name='sequence',
-    ... )
-
-    >>> df.sequence
-    0    MTEITAAMVKELRESTGAGMMDCK
-    1           SATVSEINSETDFVAKN
-    Name: sequence, dtype: object
+        >>> import tempfile
+        >>> import pandas as pd
+        >>> import janitor.biology
+
+        >>> tf = tempfile.NamedTemporaryFile()
+        >>> tf.write('''>SEQUENCE_1
+        ... MTEITAAMVKELRESTGAGMMDCK
+        ... >SEQUENCE_2
+        ... SATVSEINSETDFVAKN'''.encode('utf8'))
+        66
+        >>> tf.seek(0)
+        0
+
+        >>> df = pd.DataFrame({"sequence_accession":
+        ... ["SEQUENCE_1", "SEQUENCE_2", ]})
+
+        >>> df = df.join_fasta(
+        ...     filename=tf.name,
+        ...     id_col='sequence_accession',
+        ...     column_name='sequence',
+        ... )
+
+        >>> df.sequence
+        0    MTEITAAMVKELRESTGAGMMDCK
+        1           SATVSEINSETDFVAKN
+        Name: sequence, dtype: object
 
     :param df: A pandas DataFrame.
     :param filename: Path to the FASTA file.