[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.github/pull_request_template.md

@@ -4,10 +4,10 @@
 
 <!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->
 
--   [ ] This comment contains a description of changes (with reason)
--   [ ] Referenced issue is linked
--   [ ] If you've fixed a bug or added code that should be tested, add tests!
--   [ ] Documentation in `docs` is updated
+- [ ] This comment contains a description of changes (with reason)
+- [ ] Referenced issue is linked
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+- [ ] Documentation in `docs` is updated
 
 **Description of changes**
 

CODE_OF_CONDUCT.md

@@ -14,23 +14,23 @@ religion, or sexual identity and orientation.
 Examples of behavior that contributes to creating a positive environment
 include:
 
--   Using welcoming and inclusive language
--   Being respectful of differing viewpoints and experiences
--   Gracefully accepting constructive criticism
--   Focusing on what is best for the community
--   Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
--   The use of sexualized language or imagery and unwelcome sexual
-    attention or advances
--   Trolling, insulting/derogatory comments, and personal or political
-    attacks
--   Public or private harassment
--   Publishing others’ private information, such as a physical or
-    electronic address, without explicit permission
--   Other conduct which could reasonably be considered inappropriate in a
-    professional setting
+- The use of sexualized language or imagery and unwelcome sexual
+  attention or advances
+- Trolling, insulting/derogatory comments, and personal or political
+  attacks
+- Public or private harassment
+- Publishing others’ private information, such as a physical or
+  electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 

README.md

@@ -16,10 +16,10 @@
 
 ## Features
 
--   Exploratory and targeted analysis of Electronic Health Records
--   Quality control & preprocessing
--   Visualization & Exploration
--   Clustering & trajectory inference
+- Exploratory and targeted analysis of Electronic Health Records
+- Quality control & preprocessing
+- Visualization & Exploration
+- Clustering & trajectory inference
 
 ## Installation
 

docs/contributing.md

@@ -126,11 +126,11 @@ in the cookiecutter-scverse template.
 
 Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
 
--   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
--   Google-style docstrings
--   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
--   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
--   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- Google-style docstrings
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.
@@ -144,10 +144,10 @@ These notebooks come from [pert-tutorials](https://github.com/theislab/ehrapy-tu
 
 #### Hints
 
--   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
-    if you do so can sphinx automatically create a link to the external documentation.
--   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
-    the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+  if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+  the `nitpick_ignore` list in `docs/conf.py`
 
 #### Building the docs locally
 

docs/index.md

@@ -61,8 +61,8 @@ medRxiv 2023.12.11.23299816; doi: https://doi.org/10.1101/2023.12.11.23299816 ](
 
 # Indices and tables
 
--   {ref}`genindex`
--   {ref}`modindex`
--   {ref}`search`
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
 
 [scanpy genome biology (2018)]: https://doi.org/10.1186/s13059-017-1382-0

docs/installation.md

@@ -51,10 +51,10 @@ pip install ehrapy[medcat]
 
 Available language models are
 
--   en_core_web_md (python -m spacy download en_core_web_md)
--   en-core-sci-sm (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz>)
--   en-core-sci-md (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz>)
--   en-core-sci-lg (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz>)
+- en_core_web_md (python -m spacy download en_core_web_md)
+- en-core-sci-sm (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz>)
+- en-core-sci-md (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz>)
+- en-core-sci-lg (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz>)
 
 [github repo]: https://github.com/theislab/ehrapy
 [pip]: https://pip.pypa.io

ehrapy/plot/__init__.py

@@ -2,6 +2,6 @@
 from ehrapy.plot._colormaps import *  # noqa: F403
 from ehrapy.plot._missingno_pl_api import *  # noqa: F403
 from ehrapy.plot._scanpy_pl_api import *  # noqa: F403
-from ehrapy.plot._survival_analysis import kaplan_meier, ols, coxph_forestplot
+from ehrapy.plot._survival_analysis import coxph_forestplot, kaplan_meier, ols
 from ehrapy.plot.causal_inference._dowhy import causal_effect
 from ehrapy.plot.feature_ranking._feature_importances import rank_features_supervised

ehrapy/plot/_survival_analysis.py

@@ -3,13 +3,12 @@
 import warnings
 from typing import TYPE_CHECKING
 
-from lifelines import CoxPHFitter
-from matplotlib import gridspec
 import matplotlib.pyplot as plt
 import matplotlib.ticker as ticker
 import numpy as np
-from numpy import ndarray
 import pandas as pd
+from matplotlib import gridspec
+from numpy import ndarray
 
 from ehrapy.plot import scatter
 
@@ -18,7 +17,7 @@
     from xmlrpc.client import Boolean
 
     from anndata import AnnData
-    from lifelines import KaplanMeierFitter
+    from lifelines import CoxPHFitter, KaplanMeierFitter
     from matplotlib.axes import Axes
     from statsmodels.regression.linear_model import RegressionResults
 
@@ -297,29 +296,32 @@ def kaplan_meier(
 
     if not show:
         return ax
-      
+
     else:
         return None
 
-def coxph_forestplot(coxph: CoxPHFitter, 
-                    labels: list[str] | None = None,
-                    fig_size: tuple = (10, 10),
-                    t_adjuster: float = 0.1,
-                    ecolor: str = 'dimgray',
-                    size: int = 3,
-                    marker: str = 'o',
-                    decimal: int = 2,
-                    text_size: int = 12,
-                    color: str = 'k'):
+
+def coxph_forestplot(
+    coxph: CoxPHFitter,
+    labels: list[str] | None = None,
+    fig_size: tuple = (10, 10),
+    t_adjuster: float = 0.1,
+    ecolor: str = "dimgray",
+    size: int = 3,
+    marker: str = "o",
+    decimal: int = 2,
+    text_size: int = 12,
+    color: str = "k",
+):
     """Plots a forest plot of the Cox Proportional Hazard model.
-    Inspired by the forest plot in the zEpid package in Python. 
+    Inspired by the forest plot in the zEpid package in Python.
     Link: https://zepid.readthedocs.io/en/latest/Graphics.html#effect-measure-plots
 
     Args:
         coxph: Fitted CoxPHFitter object.
         labels: List of labels for each coefficient, default uses the index of the coxph.summary.
         fig_size: Width, height in inches.
-        t_adjuster: Adjust the table to the right. 
+        t_adjuster: Adjust the table to the right.
         ecolor: Color of the error bars.
         size: Size of the markers.
         marker: Marker style.
@@ -339,60 +341,88 @@ def coxph_forestplot(coxph: CoxPHFitter,
     """
 
     data = coxph.summary
-    auc_col = 'coef'
+    auc_col = "coef"
 
     if labels is None:
         labels = data.index
     tval = []
     ytick = []
     for i in range(len(data)):
         if not np.isnan(data[auc_col][i]):
-            if ((isinstance(data[auc_col][i], float)) & (isinstance(data['coef lower 95%'][i], float)) &
-                    (isinstance(data['coef upper 95%'][i], float))):
-                tval.append([round(data[auc_col][i], decimal), (
-                            '(' + str(round(data['coef lower 95%'][i], decimal)) + ', ' +
-                            str(round(data['coef upper 95%'][i], decimal)) + ')')])
+            if (
+                (isinstance(data[auc_col][i], float))
+                & (isinstance(data["coef lower 95%"][i], float))
+                & (isinstance(data["coef upper 95%"][i], float))
+            ):
+                tval.append(
+                    [
+                        round(data[auc_col][i], decimal),
+                        (
+                            "("
+                            + str(round(data["coef lower 95%"][i], decimal))
+                            + ", "
+                            + str(round(data["coef upper 95%"][i], decimal))
+                            + ")"
+                        ),
+                    ]
+                )
             else:
-                tval.append([data[auc_col][i], ('(' + str(data['coef lower 95%'][i]) + ', ' + str(data['coef upper 95%'][i]) + ')')])
+                tval.append(
+                    [
+                        data[auc_col][i],
+                        ("(" + str(data["coef lower 95%"][i]) + ", " + str(data["coef upper 95%"][i]) + ")"),
+                    ]
+                )
             ytick.append(i)
         else:
-            tval.append([' ', ' '])
+            tval.append([" ", " "])
             ytick.append(i)
 
-    maxi = round(((pd.to_numeric(data['coef upper 95%'])).max() + 0.1),2)  # setting x-axis maximum 
+    maxi = round(((pd.to_numeric(data["coef upper 95%"])).max() + 0.1), 2)  # setting x-axis maximum
+
+    mini = round(((pd.to_numeric(data["coef lower 95%"])).min() - 0.1), 1)  # setting x-axis minimum
 
-    mini = round(((pd.to_numeric(data['coef lower 95%'])).min() - 0.1), 1)  # setting x-axis minimum
-
     fig = plt.figure(figsize=fig_size)
     gspec = gridspec.GridSpec(1, 6)  # sets up grid
     plot = plt.subplot(gspec[0, 0:4])  # plot of data
     tabl = plt.subplot(gspec[0, 4:])  # table
     plot.set_ylim(-1, (len(data)))  # spacing out y-axis properly
-
-    plot.axvline(1, color='gray', zorder=1)
-    lower_diff = data[auc_col] - data['coef lower 95%']
-    upper_diff = data['coef upper 95%'] - data[auc_col]
-    plot.errorbar(data[auc_col], data.index, xerr=[lower_diff, upper_diff], marker='None', zorder=2, ecolor=ecolor, linewidth=0, elinewidth=1)
-    plot.scatter(data[auc_col], data.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors='None')
-    plot.xaxis.set_ticks_position('bottom')
-    plot.yaxis.set_ticks_position('left')
+
+    plot.axvline(1, color="gray", zorder=1)
+    lower_diff = data[auc_col] - data["coef lower 95%"]
+    upper_diff = data["coef upper 95%"] - data[auc_col]
+    plot.errorbar(
+        data[auc_col],
+        data.index,
+        xerr=[lower_diff, upper_diff],
+        marker="None",
+        zorder=2,
+        ecolor=ecolor,
+        linewidth=0,
+        elinewidth=1,
+    )
+    plot.scatter(data[auc_col], data.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors="None")
+    plot.xaxis.set_ticks_position("bottom")
+    plot.yaxis.set_ticks_position("left")
     plot.get_xaxis().set_major_formatter(ticker.ScalarFormatter())
     plot.get_xaxis().set_minor_formatter(ticker.NullFormatter())
     plot.set_yticks(ytick)
     plot.set_xlim([mini, maxi])
     plot.set_xticks([mini, 1, maxi])
     plot.set_xticklabels([mini, 1, maxi])
-    plot.set_yticklabels(labels) 
-    plot.tick_params(axis='y', labelsize=text_size)
-    plot.yaxis.set_ticks_position('none')
+    plot.set_yticklabels(labels)
+    plot.tick_params(axis="y", labelsize=text_size)
+    plot.yaxis.set_ticks_position("none")
     plot.invert_yaxis()  # invert y-axis to align values properly with table
-    tb = tabl.table(cellText=tval, cellLoc='center', loc='right', colLabels=[auc_col, '95% CI'], bbox=[0, t_adjuster, 1, 1])
-    tabl.axis('off')
+    tb = tabl.table(
+        cellText=tval, cellLoc="center", loc="right", colLabels=[auc_col, "95% CI"], bbox=[0, t_adjuster, 1, 1]
+    )
+    tabl.axis("off")
     tb.auto_set_font_size(False)
     tb.set_fontsize(text_size)
-    for _ , cell in tb.get_celld().items():
+    for _, cell in tb.get_celld().items():
         cell.set_linewidth(0)
     plot.spines["top"].set_visible(False)
     plot.spines["right"].set_visible(False)
     plot.spines["left"].set_visible(False)
-    return fig,  plot
+    return fig, plot

tests/_scripts/coxph_forestplot_create_expected.ipynb

@@ -16,9 +16,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import matplotlib.pyplot as plt\n",
     "\n",
-    "import ehrapy as ep\n",
-    "import matplotlib.pyplot as plt"
+    "import ehrapy as ep"
    ]
   },
   {
@@ -49,7 +49,7 @@
    "source": [
     "genderafib_coxph = ep.tl.cox_ph(adata_subset, duration_col=\"mort_day_censored\", event_col=\"censor_flg\")\n",
     "\n",
-    "fig, ax = ep.pl.coxph_forestplot(genderafib_coxph, fig_size=(12,3), t_adjuster=0.15, marker=\"o\", size=2, text_size=14)"
+    "fig, ax = ep.pl.coxph_forestplot(genderafib_coxph, fig_size=(12, 3), t_adjuster=0.15, marker=\"o\", size=2, text_size=14)"
    ]
   },
   {

tests/conftest.py

@@ -28,11 +28,13 @@ def root_dir():
 def rng():
     return np.random.default_rng(seed=42)
 
+
 @pytest.fixture
 def mimic_2():
     adata = ep.dt.mimic_2()
     return adata
 
+
 @pytest.fixture
 def mimic_2_encoded():
     adata = ep.dt.mimic_2(encoded=True)

tests/plot/test_catplot.py

@@ -15,10 +15,11 @@ def test_catplot_vanilla(adata_mini, check_same_image):
         tol=2e-1,
     )
 
+
 def test_coxph_forestplot(mimic_2, check_same_image):
     adata_subset = mimic_2[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
     coxph = ep.tl.cox_ph(adata_subset, duration_col="mort_day_censored", event_col="censor_flg")
-    fig, ax = ep.pl.coxph_forestplot(coxph, fig_size=(12,3), t_adjuster=0.15, marker="o", size=2, text_size=14)
+    fig, ax = ep.pl.coxph_forestplot(coxph, fig_size=(12, 3), t_adjuster=0.15, marker="o", size=2, text_size=14)
 
     check_same_image(
         fig=fig,