Patch (#55)

* Fix spacing issue at top of plot (fixes #48, #47) * Create notebook for some simple regression tests (closes #49) * Tidy imports using isort (closes #50) * Allowed thresholds and symbols for p-values to be passedthrough (fixes #51) * Fix different heigh and fontsize for confidence interval and p-value labels (fixes #53) * Update docs for RTD (closes #54) * Freeze matplotlib-inline dependency in setup.py (closes #56)
LSYS · Feb 10, 2023 · 30ee8d0 · 30ee8d0
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diff --git a/Makefile b/Makefile
@@ -24,11 +24,16 @@ lint:
 	mypy $(SRC_FILES) --ignore-missing-imports
 	python -m pyflakes tests/*.py $(SRC_FILES)
 	python -m pyflakes setup.py
+	isort --profile black $(BLACK_OPTS) . 
 	black forestplot/*.py $(BLACK_OPTS)
 	black forestplot/*.py $(BLACK_OPTS)
 	black tests/*.py $(BLACK_OPTS)
 	black setup.py $(BLACK_OPTS)
 
+.PHONY: docstring
+docstring: # Check docstrings using pydocstyle
+	pydocstyle --convention numpy
+
 .PHONY: prepack
 prepack: # Prepare packaging for PyPi
 prepack:

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 <div id="top"></div> 
 <h1 align="center" >
-  <strong>Forestplot</strong>
+  Forestplot
 </h1>
 <p align="center">
   <a href="https://pypi.org/project/forestplot">
@@ -13,24 +13,24 @@
 <p align="center"><img width="100%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/main.png"></p>
 
 -----------------------------------------------------------
-
 This package makes publication-ready forest plots easy to make out-of-the-box. Users provide a `dataframe` (e.g. from a spreadsheet) where rows correspond to a variable/study with columns including estimates, variable labels, and lower and upper confidence interval limits.
 Additional options allow easy addition of columns in the `dataframe` as annotations in the plot.
 
 <!---------------------- Project shields ---------------------->
 
 |    |    |
 | --- | --- |
-| Release | [![PyPI](https://img.shields.io/pypi/v/forestplot?color=blue&label=PyPI&logo=pypi&logoColor=white)](https://pypi.org/project/forestplot/) ![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/forestplot?logo=conda-forge&logoColor=white) [![GitHub release (latest by date)](https://img.shields.io/github/v/release/lsys/forestplot?color=blue&label=Latest%20release)](https://github.com/LSYS/forestplot/releases) |
+| Release | [![PyPI](https://img.shields.io/pypi/v/forestplot?color=blue&label=PyPI&logo=pypi&logoColor=white)](https://pypi.org/project/forestplot/) [![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/forestplot?logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/forestplot) [![GitHub release (latest by date)](https://img.shields.io/github/v/release/lsys/forestplot?color=blue&label=Latest%20release)](https://github.com/LSYS/forestplot/releases) |
 | Status | [![CI](https://github.com/LSYS/forestplot/actions/workflows/CI.yml/badge.svg)](https://github.com/LSYS/forestplot/actions/workflows/CI.yml) [![Notebooks](https://github.com/LSYS/forestplot/actions/workflows/nb.yml/badge.svg)](https://github.com/LSYS/forestplot/actions/workflows/nb.yml) |
 | Coverage |  [![Codecov](https://img.shields.io/codecov/c/github/lsys/forestplot?logo=codecov&logoColor=white&label=codecov)](https://app.codecov.io/gh/LSYS/forestplot) |
 | Python | [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/forestplot?label=Python%203.6%2B&logo=python&logoColor=white)](https://pypi.org/project/forestplot/) |
 | Docs | [![Read the Docs (version)](https://img.shields.io/readthedocs/forestplot/stable?label=docs&logo=readthedocs&logoColor=white)](https://forestplot.readthedocs.io/en/latest/?badge=latest) [![DocLinks](https://github.com/LSYS/forestplot/actions/workflows/links.yml/badge.svg)](https://github.com/LSYS/forestplot/actions/workflows/links.yml)|
-| Meta | ![GitHub](https://img.shields.io/github/license/lsys/forestplot?color=purple&label=License) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/LSYS/forestplot.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/LSYS/forestplot/context:python) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![types - Mypy](https://img.shields.io/badge/types-Mypy-blue.svg)](https://github.com/python/mypy) [![DOI](https://zenodo.org/badge/510013191.svg)](https://zenodo.org/badge/latestdoi/510013191) |
+| Meta | [![GitHub](https://img.shields.io/github/license/lsys/forestplot?color=purple&label=License)](https://choosealicense.com/licenses/mit/) [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![types - Mypy](https://img.shields.io/badge/types-Mypy-blue.svg)](https://github.com/python/mypy) [![DOI](https://zenodo.org/badge/510013191.svg)](https://zenodo.org/badge/latestdoi/510013191) |
 | Binder| [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/lsys/forestplot/main?labpath=examples%2Freadme-examples.ipynb) |
 
 <!---------------------- TABLE OF CONTENT ---------------------->
-<details open><summary><b>Table of Contents</b></summary><p>
+# Table of Contents[![](https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/pin.svg)](#table-of-contents)
+<details open><summary><b>show/hide</b></summary><p>
 
 > - [Installation](#installation)
 > - [Quick Start](#quick-start)
@@ -51,7 +51,7 @@ pip install forestplot
 ```
 
 Install from conda-forge<br>
-![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/forestplot?logo=conda-forge&logoColor=white)
+[![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/forestplot?logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/forestplot)
 ```bash
 conda install forestplot
 ```
@@ -78,7 +78,7 @@ make test
 
 
 <!------------------------- QUICK START ------------------------->
-## Quick start[![](https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/pin.svg)](#quick-start)
+## Quick Start[![](https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/pin.svg)](#quick-start)
 
 ```python
 import forestplot as fp
@@ -119,7 +119,7 @@ fp.forestplot(df,  # the dataframe with results data
               ll="ll", hl="hl",  # columns containing conf. int. lower and higher limits
               varlabel="label",  # column containing variable label
               ylabel="Confidence interval",  # y-label title
-              xlabel="Pearson correlation"  # x-label title
+              xlabel="Pearson correlation",  # x-label title
               )
 ```
 <p align="left"><img width="55%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/vanilla.png"></p>
@@ -131,8 +131,7 @@ plt.savefig("plot.png", bbox_inches="tight")
 <p align="right">(<a href="#top">back to top</a>)</p>
 
 <!------------------ EXAMPLES of CUSTOMIZATIONS ------------------>
-## Some examples with customizations[![](https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/pin.svg)](#examples-with-customizations)
-
+## Some Examples With Customizations[![](https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/pin.svg)](#examples-with-customizations)
 
 1. Add variable groupings, add group order, and sort by estimate size.
 ```python
@@ -145,10 +144,10 @@ fp.forestplot(df,  # the dataframe with results data
               # group ordering
               group_order=["labor factors", "occupation", "age", "health factors", 
                            "family factors", "area of residence", "other factors"],
-              sort=True  # sort in ascending order (sorts within group if group is specified)               
+              sort=True,  # sort in ascending order (sorts within group if group is specified)               
               )
 ```
-<p align="left"><img width="65%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/group-grouporder-sort.png"></p>
+<p align="left"><img width="75%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/group-grouporder-sort.png"></p>
 
 2. Add p-values on the right and color alternate rows gray
 ```python
@@ -169,7 +168,7 @@ fp.forestplot(df,  # the dataframe with results data
               )
 ```
 
-<p align="left"><img width="70%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/group-grouporder-pvalue-sort-colorrows.png"></p>
+<p align="left"><img width="80%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/group-grouporder-pvalue-sort-colorrows.png"></p>
 
 
 3. Customize annotations and make it a table
@@ -189,7 +188,7 @@ fp.forestplot(df,  # the dataframe with results data
               )
 ```
 
-<p align="left"><img width="75%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/leftannote-rightannote-table.png"></p>
+<p align="left"><img width="85%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/leftannote-rightannote-table.png"></p>
 
 4. Strip down all bells and whistle
 ```python
@@ -233,7 +232,7 @@ fp.forestplot(df,  # the dataframe with results data
                 }  
               )
 ```
-<p align="left"><img width="70%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/main.png"></p>
+<p align="left"><img width="80%" src="https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/main.png"></p>
 
 <details><summary><i>Annotations arguments allowed include:</i></summary>
 
@@ -307,8 +306,10 @@ More fined-grained control for base plot options (eg font sizes, marker colors)
 
 <!------------------------ KNOWN ISSUES ------------------------>
 ## Known Issues[![](https://raw.githubusercontent.com/LSYS/forestplot/main/docs/images/pin.svg)](#known-issues)
+
 * Variable labels coinciding with group variables may lead to unexpected formatting issues in the graph.
 * Left-flushing of annotations relies on the `monospace` font.
+* Plot may give strange behavior for few rows of data (six rows or fewer. [see this issue](https://github.com/LSYS/forestplot/issues/52))
 * Plot can get cluttered with too many variables/rows (~30 onwards) 
 <p align="right">(<a href="#top">back to top</a>)</p>
 

diff --git a/codecov.yml b/codecov.yml
@@ -5,4 +5,5 @@ coverage:
         target: auto
         # adjust accordingly based on how flaky your tests are
         # this allows a 10% drop from the previous base commit coverage
-        threshold: 50%  # Relax my coverage target, because I have flaky tests
+        threshold: 10%  # Relax my coverage target, because I have flaky tests
+    patch: off
diff --git a/docs/README.rst b/docs/README.rst
diff --git a/docs/assets/issue52-table-does-not-work-6rows-or-fewer.ipynb b/docs/assets/issue52-table-does-not-work-6rows-or-fewer.ipynb
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,3 +1,4 @@
+"""Config file for Sphinx."""
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full
@@ -17,8 +18,8 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'pyForestplot'
-copyright = '2022, Lucas Shen'
+project = 'Forestplot'
+copyright = '2023, Lucas Shen'
 author = 'Lucas Shen'
 
 # The full version, including alpha/beta/rc tags
@@ -33,7 +34,7 @@
 extensions = [
 	'myst_parser'
 ]
-
+myst_heading_anchors = 2
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -49,7 +50,16 @@
 # a list of builtin themes.
 #
 html_theme = 'furo'
-
+html_sidebars = {
+    "**": [
+        "sidebar/scroll-start.html",
+        "sidebar/brand.html",
+        "sidebar/search.html",
+        "sidebar/navigation.html",
+        "sidebar/ethical-ads.html",
+        "sidebar/scroll-end.html",
+    ]
+}
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".

diff --git a/docs/images/group-grouporder-pvalue-sort-colorrows.png b/docs/images/group-grouporder-pvalue-sort-colorrows.png
diff --git a/docs/images/group-grouporder-sort.png b/docs/images/group-grouporder-sort.png
diff --git a/docs/images/leftannote-rightannote-table.png b/docs/images/leftannote-rightannote-table.png
diff --git a/docs/images/main.png b/docs/images/main.png
diff --git a/docs/images/vanilla.png b/docs/images/vanilla.png
diff --git a/docs/images/vcoefplot.png b/docs/images/vcoefplot.png
diff --git a/docs/index.md b/docs/index.md
@@ -8,5 +8,5 @@
 
 ```{toctree}
 :caption: 'Contents:'
-:maxdepth: 1
+:maxdepth: 2
 ```
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,3 @@
 myst_parser
-furo
+furo
+forestplot
diff --git a/examples/data/regression1.csv b/examples/data/regression1.csv
@@ -0,0 +1 @@
+varname,or,low,higha,1.761471,0.926563,3.022285b,1.44366,0.517059,3.130794c,1.525227,0.603459,3.082003d,0.895682,0.463703,1.660016e,4.02567,1.196941,8.932753f,1.086105,0.555171,2.045735

diff --git a/examples/readme-examples.ipynb b/examples/readme-examples.ipynb
diff --git a/forestplot/__init__.py b/forestplot/__init__.py
@@ -1,6 +1,7 @@
-VERSION = (0, 2, 1)
+"""State version and import user-facing functions."""
+VERSION = (0, 2, 2)
 
 __version__ = ".".join(map(str, VERSION))
 
-from forestplot.plot import forestplot
 from forestplot.dataframe_utils import load_data
+from forestplot.plot import forestplot
diff --git a/forestplot/arg_validators.py b/forestplot/arg_validators.py
@@ -1,7 +1,9 @@
-import pandas.api.types as ptypes
-import pandas as pd
-from typing import Optional, Union, Sequence
+"""Holds functions to check data and validate arguments from users."""
 import warnings
+from typing import Optional, Sequence, Union
+
+import pandas as pd
+import pandas.api.types as ptypes
 
 
 def check_data(
@@ -19,46 +21,45 @@ def check_data(
     pval: Optional[str] = None,
     ylabel2: Optional[str] = None,
 ) -> pd.core.frame.DataFrame:
-    """
-        Checks and validate that dataframe has the correct data. If data is missing, create them.
+    """Check and validate that dataframe has the correct data. If data is missing, create them.
 
     Checks and validates key arguments.
 
-        Parameters
-        ----------
-        dataframe (pandas.core.frame.DataFrame)
-                Pandas DataFrame where rows are variables. Columns are variable name, estimates,
-                margin of error, etc.
-        estimate (str)
-                Name of column containing the estimates (e.g. pearson correlation coefficient,
-                OR, regression estimates, etc.).
-        varlabel (str)
-                Name of column containing the variable label to be printed out.
-        groupvar (str)
-                Name of column containing group of variables.
-        group_order (list-like)
-                List of groups by order to report in the figure.
-        ll (str)
-                Name of column containing the lower limit of the confidence intervals.
-        hl (str)
-                Name of column containing the upper limit of the confidence intervals.
-        annote (list-like)
-                List of columns to add as additional annotation in the plot.
-        annoteheaders (list-like)
-                List of table headers to use as column headers for the additional annotations.
-        rightannote (list-like)
-                List of columns to add as additional annotation on the right-hand side of the plot.
-        right_annoteheaders (list-like)
-                List of table headers to use as column headers for the additional annotations
-                on the right-hand side of the plot.
-        pval (str)
-                Name of column containing the p-values.
-        ylabel2 (str)
-                Title of the right-hand side y-axis.
-
-        Returns
-        -------
-                pd.core.frame.DataFrame.
+    Parameters
+    ----------
+    dataframe (pandas.core.frame.DataFrame)
+            Pandas DataFrame where rows are variables. Columns are variable name, estimates,
+            margin of error, etc.
+    estimate (str)
+            Name of column containing the estimates (e.g. pearson correlation coefficient,
+            OR, regression estimates, etc.).
+    varlabel (str)
+            Name of column containing the variable label to be printed out.
+    groupvar (str)
+            Name of column containing group of variables.
+    group_order (list-like)
+            List of groups by order to report in the figure.
+    ll (str)
+            Name of column containing the lower limit of the confidence intervals.
+    hl (str)
+            Name of column containing the upper limit of the confidence intervals.
+    annote (list-like)
+            List of columns to add as additional annotation in the plot.
+    annoteheaders (list-like)
+            List of table headers to use as column headers for the additional annotations.
+    rightannote (list-like)
+            List of columns to add as additional annotation on the right-hand side of the plot.
+    right_annoteheaders (list-like)
+            List of table headers to use as column headers for the additional annotations
+            on the right-hand side of the plot.
+    pval (str)
+            Name of column containing the p-values.
+    ylabel2 (str)
+            Title of the right-hand side y-axis.
+
+    Returns
+    -------
+            pd.core.frame.DataFrame.
     """
     ##########################################################################
     ## Check that numeric data are numeric
@@ -203,7 +204,7 @@ def check_data(
 
 
 def check_iterables_samelen(*args):  # type: ignore
-    """Assert that provided iterables have same length"""
+    """Assert that provided iterables have same length."""
     try:
         assert all(len(args[0]) == len(_arg) for _arg in args[1:])
     except Exception:
@@ -214,8 +215,7 @@ def check_iterables_samelen(*args):  # type: ignore
 def check_groups(
     dataframe: pd.core.frame.DataFrame, groupvar: str, group_order: Optional[Sequence]
 ) -> None:
-    """
-    Check that provided group-related args are well-behaved.
+    """Check that provided group-related args are well-behaved.
 
     Parameters
     ----------
@@ -226,6 +226,7 @@ def check_groups(
         Name of column containing group of variables.
     group_order (list-like)
         List of groups by order to report in the figure.
+
     Returns
     -------
     None

diff --git a/forestplot/dataframe_utils.py b/forestplot/dataframe_utils.py
@@ -1,6 +1,8 @@
-import pandas as pd
+"""Holds functions to check prepare dataframe for plotting."""
+from typing import Any, Optional, Union
+
 import numpy as np
-from typing import Optional, Union, Any
+import pandas as pd
 
 
 def insert_groups(