1 scripts running for too long

.github/workflows/build.yml

@@ -15,28 +15,30 @@ jobs:
       matrix:
         python-version: ["3.10", "3.9"]
 
-      steps:
-        - name: Checkout repo
-          uses: actions/checkout@v4
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          lfs: true
 
-        - name: Install miniconda
-          uses: conda-incubator/setup-miniconda@v2
-          with:
-            miniconda-version: "latest"
-            auto-update-conda: true
-            python-version: ${{ matrix.python-version }}
+      - name: Install miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
 
-        - name: Initialize conda environment
-          run: make conda-create
+      - name: Initialize conda environment
+        run: make conda-create
 
-        - name: Setup conda
-          run: make conda-setup
+      - name: Setup conda
+        run: make conda-setup
 
-        - name: Install conda dependencies
-          run: make from-conda-lock
+      - name: Install conda dependencies
+        run: make from-conda-lock
 
-        - name: Poetry install
-          run: make install
+      - name: Poetry install
+        run: make install
 
-        - name: Run tests
-          run: make test
+      - name: Run tests
+        run: make test

.github/workflows/codecov.yml

@@ -16,6 +16,8 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
+        with:
+          lfs: true
 
       - name: Install miniconda
         uses: conda-incubator/setup-miniconda@v2

.github/workflows/deploy-docs.yml

@@ -54,7 +54,7 @@ jobs:
         run: make install
 
       - name: Build documentation
-        run: make docs-versioned
+        run: make docs
 
       - name: Setup Pages
         uses: actions/configure-pages@v3

.gitignore

@@ -109,6 +109,7 @@ ENV/
 docs/source/_build
 docs/html
 docs/source/doc
+public/
 
 # psi4
 timer.dat
@@ -118,8 +119,4 @@ psi.*.clean
 tests/tmp/
 tests/files/tmp/*
 !tests/files/tmp/.gitkeep
-
-# Reptar data
-examples/reptar-data
-
-docs/source/autoapi
+report.xml

CHANGELOG.md

@@ -4,6 +4,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 
 ## [Unreleased]
 
+### Added
+
+- Will keep track of `TER` in frames to correctly handle assigning chain IDs.
+- Check for combinatorial explosions.
+
 ### Changed
 
 - Modularized code and set up for deploying to PyPI.

README.md

@@ -16,10 +16,24 @@ TODO: check that the VMD plugin installation works.
    - `vmd_install_extension wisp wisp_tk_cb "Analysis/Wisp"`
 2. Now open VMD: Click Extensions > Analysis > WISP
 
-## How to Use WISP from the Command Line
+## Usage
+
+You may use the `wisp` command-line interface as shown below.
+
+```bash
+wisp -pdb_trajectory_filename tests/files/trajectory_20_frames.pdb -source_residues "C_LEU_10" -sink_residues C_ASP_11
+```
+
+Or, you may use wisp as a library in Python.
 
 ```python
-wisp -pdb_trajectory_filename multi_frame_pdb.pdb -source_residues "X_SER_1 X_LEU_4" -sink_residues X_ARG_37`
+from wisp.run import run_wisp
+config = {
+    "pdb_trajectory_filename": "tests/files/trajectory_20_frames.pdb",
+    "source_residues": ["C_LEU_10"],
+    "sink_residues": ["C_ASP_11"],
+}
+paths = run_wisp(config)
 ```
 
 ## Program Output

tests/test_wisp.py

@@ -1,16 +1,16 @@
 import os
 import shutil
-import subprocess
 
 import numpy as np
+import pytest
 
 from wisp.run import run_wisp
 
 # Ensures we execute from file directory (for relative paths).
-os.chdir(os.path.dirname(os.path.realpath(__file__)))
+current_dir = os.path.dirname(os.path.abspath(__file__))
 
-FILE_DIR = "./files/"
-WRITING_DIR = "./tmp/"
+FILE_DIR = os.path.join(current_dir, "files/")
+WRITING_DIR = os.path.join(current_dir, "tmp/")
 
 
 def test_example():
@@ -49,7 +49,7 @@ def test_example():
         "spline_smoothness": 0.01,
         "vmd_resolution": 6,
         "output_directory": test_dir,
-        "logfile": open(os.path.join(test_dir, "log.txt"), "w"),
+        "logfile": open(os.path.join(test_dir, "log.txt"), "w", encoding="utf-8"),
         "user_specified_contact_map_filename": "",
         "user_specified_functionalized_matrix_filename": "",
         "simply_formatted_paths_filename": os.path.join(
@@ -114,40 +114,18 @@ def test_issue_1_serial():
         "shortest_path_opacity": 1.0,
         "shortest_path_r": 0.0,
         "shortest_path_radius": 1.0,
-        "sink_residues": ["A_HIE_840"],
-        "source_residues": ["A_ASN_692"],
+        "sink_residues": ["C_HIE_840"],
+        "source_residues": ["B_ASN_692"],
         "spline_smoothness": 0.01,
         "vmd_resolution": 6,
         "output_directory": test_dir,
-        "logfile": open(os.path.join(test_dir, "log.txt"), "w"),
+        "logfile": open(os.path.join(test_dir, "log.txt"), "w", encoding="utf-8"),
         "user_specified_contact_map_filename": "",
         "user_specified_functionalized_matrix_filename": "",
         "simply_formatted_paths_filename": os.path.join(
             test_dir, "simply_formatted_paths.txt"
         ),
         "pdb_single_frame_filename": "",
     }
-    paths = run_wisp(config)
-    test_data = np.array([i[0] for i in paths], dtype=np.float64)
-
-    # ref_data = np.array(
-    #     [
-    #         1.1363589537262389,
-    #         2.027418997284591,
-    #         2.205901870787125,
-    #         2.307449850568712,
-    #         2.442623103273746,
-    #         2.448087831142992,
-    #         2.501932824731498,
-    #         2.5026984744745864,
-    #         2.621657347053458,
-    #         2.6370708377784413,
-    #         2.6804156982340315,
-    #         2.7056328296310643,
-    #         2.8932868716011986,
-    #         2.977212301921493,
-    #         3.0311375788312436,
-    #     ],
-    #     dtype=np.float64,
-    # )
-    # assert np.allclose(test_data, ref_data)
+    with pytest.raises(SystemExit) as e:
+        run_wisp(config)

wisp/io.py

@@ -2,13 +2,16 @@
 
 
 def output_directory_info(params):
-    """Create a README.txt file in the output directory describing the directory contents
+    """Create a README.txt file in the output directory describing the directory
+    contents.
 
-    Arguments:
-    params -- the user-specified command-line parameters, a UserInput object
+    Args:
+        params: The user-specified command-line parameters, a UserInput object
     """
 
-    f = open(os.path.join(params["output_directory"], "README.txt"), "w")
+    f = open(
+        os.path.join(params["output_directory"], "README.txt"), "w", encoding="utf-8"
+    )
     f.write(
         "This directory contains output from the program WISP. The best way to visualize the output is to use a free program called VMD, which can be downloaded from http://www.ks.uiuc.edu/Research/vmd/ ."
         + "\n\n"