Move tests into package

.flake8

@@ -16,4 +16,5 @@ ignore =
 exclude=
     .git,
     venv,
-    tests/test_data,
+    test_data,
+    test_output,

.github/workflows/tests.yml

@@ -36,21 +36,13 @@ jobs:
     - name: Check code style with flake8
       if: ${{ matrix.python-version == env.python-latest }}
       run: |
-        python -m flake8 pcpostprocess/*.py tests/*.py pcpostprocess/scripts/*.py
-
-    - name: Check import ordering with isort
-      if: ${{ matrix.python-version == env.python-latest }}
-      run: |
-        python -m isort --verbose --check-only --diff pcpostprocess tests setup.py
+        python -m flake8 pcpostprocess
 
     - name: Extract test data
       run: |
-        wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
-        tar xvf tests/test_data.tar.xz -C tests/
-
-    - name: Install TeX dependencies for run_herg_qc test
-      timeout-minutes: 5
-      run: sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
+        wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz
+        tar xvf test_data.tar.xz
+        rm test_data.tar.xz
 
     - name: Run unit tests (without coverage testing)
       if: ${{ success() && matrix.python-version != env.python-latest }}

.gitignore

@@ -1,8 +1,28 @@
+# Autogenerated by setuptools-wcm
 pcpostprocess/_version.py
-/tests/test_data
+
+# Tests and test data
+.coverage
+/test_data
 /test_output
 /output
-*__pycache__*
+
+# Compiled python
+*.pyc
+__pycache__
+
+# Installation files
 *.egg-info
-*.DS_Store
-.coverage
+
+# Jupyter notebooks
+.ipynb_checkpoints
+
+# Virtual environments
+venv
+env
+
+# DS Store
+.DS_Store
+
+# VS code config
+.vscode

CHANGELOG.md

@@ -5,9 +5,10 @@ This page lists the main changes made to pcpostprocess in each release.
 ## Unreleased
 - Added
   - [#81](https://github.com/CardiacModelling/pcpostprocess/pull/81) Added docstrings to the `hERGQC` class.
-  - [#104](https://github.com/CardiacModelling/pcpostprocess/pull/104) Added a CHANGELOG.md and CONTRIBUTING.md
+  - [#104](https://github.com/CardiacModelling/pcpostprocess/pull/104) Added a CHANGELOG.md and CONTRIBUTING.md.
 - Changed
   - [#81](https://github.com/CardiacModelling/pcpostprocess/pull/81) Changed the constructor arguments for `hERGQC`.
+  - [#122](https://github.com/CardiacModelling/pcpostprocess/pull/122) `fit_linear_leak` no longer accepts an `output_dir` argument.
 - Deprecated
 - Removed
  - [#81](https://github.com/CardiacModelling/pcpostprocess/pull/81) Removed `hERGQC.plot_dir`, `hERGQC.set_trace` and `hERGQC.set_debug`.

CONTRIBUTING.md

@@ -62,17 +62,6 @@ In addition to the rules checked by flake8, we try to use single quotes (`'`) fo
 
 Class, method, and argument names are in UK english.
 
-### Import ordering
-
-Import ordering is tested with [isort](https://pycqa.github.io/isort/index.html).
-
-To run locally, use
-```
-isort --check-only --verbose ./pcpostprocess ./tests/
-```
-
-Isort is configured in [pyproject.toml](./pyproject.toml) under the section `tool.isort`.
-
 ## Documentation
 
 Every method and every class should have a [docstring](https://www.python.org/dev/peps/pep-0257/) that describes in plain terms what it does, and what the expected input and output is.

README.md

@@ -34,9 +34,9 @@ To run the tests you must first download some test data.
 Test data is available at [cardiac.nottingham.ac.uk/syncropatch\_export](https://cardiac.nottingham.ac.uk/syncropatch_export)
 
 ```sh
-wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
-tar xvf tests/test_data.tar.xz -C tests/
-rm tests/test_data.tar.xz
+wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz
+tar xvf test_data.tar.xz
+rm test_data.tar.xz
 ```
 
 Then you can run the tests.

pcpostprocess/directory_builder.py

@@ -10,43 +10,27 @@ def get_git_revision_hash():
     Get the hash for the git commit currently being used.
 
     @return The most recent commit hash or a suitable message
-
     """
-
     return __commit_id__
 
 
 def get_build_type():
-    if "dev" in __version__:
-        return "Develop"
-    else:
-        return "Release"
+    return 'Develop' if 'dev' in __version__ else 'Release'
 
 
-def setup_output_directory(dirname: str = None, subdir_name: str = None):
+def setup_output_directory(dirname: str):
     """
     Create an output directory if one doesn't already exist. Place an info
     file in this directory which lists the date/time created, the version of
     pcpostprocess, the command-line arguments provided, and the most recent git
     commit. The two parameters allow for a user specified top-level directory and
     a script-defined name for a subdirectory.
 
-    @param Optional directory name
-    @param Optional subdirectory name
+    @param Directory name
 
     @return The path to the created file directory (String)
     """
-
-    if dirname is None:
-        if subdir_name:
-            dirname = os.path.join("output", f"{subdir_name}")
-        else:
-            dirname = os.path.join("output", "output")
-
-    if subdir_name is not None:
-        dirname = os.path.join(dirname, subdir_name)
-    if not os.path.exists(dirname):
-        os.makedirs(dirname)
+    os.makedirs(dirname, exist_ok=True)
 
     with open(os.path.join(dirname, "pcpostprocess_info.txt"), "w") as description_fout:
         git_hash = get_git_revision_hash()

pcpostprocess/hergQC.py

@@ -75,13 +75,8 @@ def __init__(self, voltage, sampling_rate=5, removal_time=5, noise_len=200,
         self.removal_time = removal_time
         self.noise_len = int(noise_len)
 
-        # Passing in a plot dir enables debug mode
         self._plot_dir = plot_dir
         self.logger = logging.getLogger(__name__)
-        if self._plot_dir is not None:
-            self.logger.setLevel(logging.DEBUG)
-            # https://github.com/CardiacModelling/pcpostprocess/issues/42
-        self._plot_dir = plot_dir
 
         # Define all thresholds
 
@@ -499,8 +494,7 @@ def qc6(self, recording1, win, label=None):
         i, f = win
         val = np.mean(recording1[i:f])
         valc = self.negative_tolc * np.std(recording1[:self.noise_len])
-        if (val < valc) or not (np.isfinite(val)
-                                and np.isfinite(valc)):
+        if (val < valc) or not (np.isfinite(val) and np.isfinite(valc)):
             self.logger.debug(f'qc6_{label} val:  {val}, valc: {valc}')
             result = False
         else:

pcpostprocess/infer_reversal.py

@@ -1,5 +1,4 @@
 import logging
-import os
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -65,9 +64,6 @@ def infer_reversal_potential(current, times, voltage_segments, voltages,
 
     # Optional plot
     if output_path is not None:
-        dirname = os.path.dirname(output_path)
-        if not os.path.exists(dirname):
-            os.makedirs(dirname)
 
         fig = plt.figure(figsize=figsize)
         ax = fig.subplots()

pcpostprocess/leak_correct.py

@@ -1,6 +1,6 @@
-import logging
-import os
-
+#
+# Leak correction methods
+#
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -55,7 +55,7 @@ def get_leak_corrected(current, voltages, times, ramp_start_index,
 
 
 def fit_linear_leak(current, voltage, times, ramp_start_index, ramp_end_index,
-                    save_fname=None, output_dir=None, figsize=(5.54, 7)):
+                    save_fname=None, figsize=(5.54, 7)):
     """
     Fits linear leak to a leak ramp, returning
 
@@ -64,8 +64,6 @@ def fit_linear_leak(current, voltage, times, ramp_start_index, ramp_end_index,
     @param ramp_start_index: the index of the observation where the leak ramp begins
     @param ramp_end_index: the index of the observation where the leak ramp ends
     @param save_fname: if set, a debugging figure will be made and stored with this name
-    @param output_dir: if ``save_fname`` is set, this directory will be used to store
-    the figure, and created if it does not exist
     @param figsize: if ``save_fname`` is set, the figure size.
 
     @return: the linear regression parameters obtained from fitting the leak
@@ -106,26 +104,26 @@ def fit_linear_leak(current, voltage, times, ramp_start_index, ramp_end_index,
         time_range = (0, times.max() / 5)
 
         #  Current vs time
-        ax1.set_title(r'\textbf{a}', loc='left', usetex=True)
+        ax1.set_title(r'\textbf{a}', loc='left')
         ax1.set_xlabel(r'$t$ (ms)')
         ax1.set_ylabel(r'$I_\mathrm{obs}$ (pA)')
         ax1.set_xticklabels([])
         ax1.set_xlim(*time_range)
 
         # Voltage vs time
-        ax2.set_title(r'\textbf{b}', loc='left', usetex=True)
+        ax2.set_title(r'\textbf{b}', loc='left')
         ax2.set_xlabel(r'$t$ (ms)')
         ax2.set_ylabel(r'$V_\mathrm{cmd}$ (mV)')
         ax2.set_xlim(*time_range)
 
         # Current vs voltage
-        ax3.set_title(r'\textbf{c}', loc='left', usetex=True)
+        ax3.set_title(r'\textbf{c}', loc='left')
         ax3.set_xlabel(r'$V_\mathrm{cmd}$ (mV)')
         ax3.set_ylabel(r'$I_\mathrm{obs}$ (pA)')
 
         ax4.set_xlabel(r'$t$ (ms)')
         ax4.set_ylabel(r'current (pA)')
-        ax4.set_title(r'\textbf{d}', loc='left', usetex=True)
+        ax4.set_title(r'\textbf{d}', loc='left')
 
         start_t = times[ramp_start_index]
         end_t = times[ramp_end_index]
@@ -152,14 +150,8 @@ def fit_linear_leak(current, voltage, times, ramp_start_index, ramp_end_index,
                  alpha=0.5, label=r'$I_\mathrm{obs} - I_\mathrm{L}$')
         ax4.legend(frameon=False)
 
-        if not os.path.exists(output_dir):
-            os.makedirs(output_dir)
-
-        if output_dir:
-            try:
-                fig.savefig(os.path.join(output_dir, save_fname))
-                plt.close(fig)
-            except Exception as exc:
-                logging.warning(str(exc))
+        if save_fname is not None:
+            fig.savefig(save_fname)
+            plt.close(fig)
 
     return (b_0, b_1), I_leak