Merge pull request #9 from harmsm/main

added unit test

.github/workflows/python-app.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and flake8 across
+# platforms and python versions. 
+
+name: ElliptiCBn
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        os: [ubuntu-latest,macos-latest,windows-latest]
+        python-version: ['3.7', '3.8', '3.9', '3.10' , '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: install ElliptiCBn
+      run: |
+        # platform specific packages
+        python -m pip install . -vv -r requirements.txt
+
+    - name: run flake8
+      run: |
+        pip install flake8
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+
+    - name: run pytest coverage 
+      run: |
+        pip install pytest
+        pytest tests/

ElliptiCBn/core.py

@@ -156,6 +156,10 @@ def get_macrocycles(filename,
 
     print(f'Analyzing {filename}.',flush=True)
 
+    if min_num_carbons >= max_num_carbons:
+        err = f"min_num_carbons ({min_num_carbons}) must be smaller than max_num_carbons ({max_num_carbons})\n"
+        raise ValueError(err)
+
     allowed_atoms = ["C","N","O","H"]
     chno_lines = []
     non_chno_dict = {"atom_type":[],
@@ -604,10 +608,10 @@ def plot_results(atom_df,
                           yaxis_visible=False,
                           zaxis_visible=False)
 
-    # Save html if requested
-    if html_file is not None:
-        print(f"Saving plot to {html_file}",flush=True)
-        fig.write_html(html_file)
+        # Save html if requested
+        if html_file is not None:
+            print(f"Saving plot to {html_file}",flush=True)
+            fig.write_html(html_file)
 
     return fig
 

run_all_tests.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+echo "Running flake8"
+flake_test=`flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics`
+if [[ "${flake_test}" != 0 ]]; then
+    echo "flake failed"
+    exit
+fi
+
+rm -rf reports
+mkdir reports
+mkdir reports/junit
+mkdir reports/coverage
+mkdir reports/badges
+
+echo "Running flake8, aggressive"
+flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics > reports/flake.txt
+
+echo "Running coverage.py"
+coverage erase
+coverage run --branch -m pytest --junit-xml=reports/junit/junit.xml
+
+echo "Generating reports"
+coverage html
+mv htmlcov reports
+
+coverage xml
+mv coverage.xml reports/coverage/coverage.xml
+

setup.py

@@ -13,9 +13,9 @@
 #Package meta-data
 DESCRIPTION= \
 """ Python package for analyzing ellipticity in CBn crystal structures. """
-URL = "https://github.com/harmslab/ElliptiCBn"  # temp URL
-EMAIL = "mshavlik@uoregon.edu"
-AUTHOR = "Michael Shavlik"
+URL = "https://github.com/harmslab/ElliptiCBn" 
+EMAIL = "harms@uoregon.edu; mshavlik@uoregon.edu"
+AUTHOR = "Michael J. Harms; Michael Shavlik"
 REQUIRES_PYTHON = ">=3.7.0"
 
 about = {}

tests/conftest.py

@@ -0,0 +1,83 @@
+import pytest
+import os
+import glob
+
+def get_files(base_dir):
+    """
+    Traverse base_dir and return a dictionary that keys all files and some
+    rudimentary *.ext expressions to absolute paths to those files. They keys
+    will be things like "some_dir/test0/rocket.txt" mapping to
+    "c:/some_dir/life/base_dir/some_dir/test0/rocket.txt". The idea is to have
+    easy-to-read cross-platform keys within unit tests.
+
+    Classes of keys:
+
+        + some_dir/test0/rocket.txt maps to a file (str)
+        + some_dir/test0/ maps to the test0 directory itself (str)
+        + some_dir/test0/*.txt maps to all .txt (list)
+        + some_dir/test0/* maps to all files or directories in the directory
+          (list)
+
+    Note that base_dir is *not* included in the keys. All are relative to that
+    directory by :code:`os.path.basename(__file__)/{base_dir}`.
+
+    Parameters
+    ----------
+    base_dir : str
+        base directory for search. should be relative to test file location.
+
+    Returns
+    -------
+    output : dict
+        dictionary keying string paths to absolute paths
+    """
+
+    containing_dir = os.path.dirname(os.path.realpath(__file__))
+    starting_dir = os.path.abspath(os.path.join(containing_dir,base_dir))
+
+    base_length = len(starting_dir.split(os.sep))
+
+    # Traverse starting_dir
+    output = {}
+    for root, dirs, files in os.walk(starting_dir):
+
+        # path relative to base_dir as a list
+        this_path = root.split(os.sep)[base_length:]
+
+        # Build paths to specific files
+        local_files = []
+        for file in files:
+            local_files.append(os.path.join(root,file))
+            new_key = this_path[:]
+            new_key.append(file)
+            output["/".join(new_key)] = local_files[-1]
+
+        # Build paths to patterns of file types
+        patterns = {}
+        ext = list(set([f.split(".")[-1] for f in local_files]))
+        for e in ext:
+            new_key = this_path[:]
+            new_key.append(f"*.{e}")
+            output["/".join(new_key)] = glob.glob(os.path.join(root,f"*.{e}"))
+
+        # Build path to all files in this directory
+        new_key = this_path[:]
+        new_key.append("*")
+        output["/".join(new_key)] = glob.glob(os.path.join(root,f"*"))
+
+        # Build paths to directories in this directory
+        for this_dir in dirs:
+            new_key = this_path[:]
+            new_key.append(this_dir)
+            # dir without terminating /
+            output["/".join(new_key)] = os.path.join(root,this_dir)
+
+            # dir with terminating /
+            new_key.append("")
+            output["/".join(new_key)] = os.path.join(root,this_dir)
+
+    return output
+
+@pytest.fixture(scope="module")
+def example_xyz():
+    return get_files(os.path.join("data","example-xyz"))