Merge pull request #52 from CovertLab/name_change

Rename arrow module to stochastic_arrow

.github/workflows/pytest.yml

@@ -0,0 +1,83 @@
+# Modified from GitHub Actions template
+
+name: Pytest
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test-on-ubuntu:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install numpy
+        pip install -r requirements.txt
+    - name: Compile Cython
+      run: |
+        make clean compile
+    - name: Test with pytest
+      run: |
+        pytest
+  test-on-windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install numpy
+        pip install -r requirements.txt
+    - name: Compile Cython
+      run: |
+        make clean compile
+    - name: Test with pytest
+      run: |
+        pytest
+  test-on-mac:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install numpy
+        pip install -r requirements.txt
+    - name: Compile Cython
+      run: |
+        make clean compile
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

@@ -10,8 +10,9 @@ profile
 /.idea/
 /tmp/
 
-arrow/arrowhead.c
-arrow/*.html
+stochastic_arrow/arrowhead.c
+stochastic_arrow/arrowhead.*.pyd
+stochastic_arrow/*.html
 
 arrow.egg-info/
 stochastic_arrow.egg-info/

MANIFEST.in

@@ -1,2 +1,2 @@
-include arrow/obsidian.h
-include arrow/mersenne.h
+include stochastic_arrow/obsidian.h
+include stochastic_arrow/mersenne.h

Makefile

@@ -2,7 +2,9 @@
 .DEFAULT_GOAL := compile
 
 clean:
-	rm -rf arrow/arrowhead*.so arrow/arrowhead.c arrow/arrowhead.html build/ dist/ MANIFEST .pytest_cache/ stochastic_arrow.egg-info/
+	### Files for older versions of stochastic_arrow are in arrow folder
+	rm -rf arrow/arrowhead*.so arrow/arrowhead.c arrow/arrowhead.html
+	rm -rf stochastic_arrow/arrowhead*.so stochastic_arrow/arrowhead.c stochastic_arrow/arrowhead.html build/ dist/ MANIFEST .pytest_cache/ stochastic_arrow.egg-info/
 	find . -name "*.pyc" -delete
 	find . -name "__pycache__" -delete
 

README.md

@@ -21,14 +21,21 @@ Add the following to your `requirements.txt`, or run
 
     stochastic-arrow
 
+**NOTE:** If upgrading from a version older than 1.0.0, check if the [`arrow`](https://github.com/arrow-py/arrow) datetime package is installed. If so, uninstall `arrow` before upgrading `stochastic-arrow`, then reinstall `arrow`.
+
+    > pip show arrow
+    > pip uninstall arrow
+    > pip install stochastic-arrow
+    > pip install arrow
+
 ## Usage
 
-The `arrow` library presents a single class as an interface,
+The `stochastic_arrow` library presents a single class as an interface,
 `StochasticSystem`, which operates on a set of reactions (encoded as a `numpy`
 matrix of stoichiometrix coefficients) and associated reaction rates:
 
 ```python
-from arrow import StochasticSystem
+from stochastic_arrow import StochasticSystem
 import numpy as np
 
 # Each row is a reaction and each column is a molecular species (or other
@@ -79,14 +86,14 @@ derived from the list of events and the stoichiometric matrix, along with the in
 state. `reenact_events` will do this for you:
 
 ```python
-from arrow import reenact_events
+from stochastic_arrow import reenact_events
 
-history = reenact_events(stoichiometry, result['events'], state)
+history = reenact_events(stoichiometric_matrix, result['events'], state)
 ```
 
 ## Testing
 
-`arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
+`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
 
     > make clean compile
     > pytest
@@ -95,26 +102,30 @@ history = reenact_events(stoichiometry, result['events'], state)
 
 There are more command line features in test_arrow:
 
-    > python -m arrow.test.test_arrow --complexation
+    > python -m stochastic_arrow.test.test_arrow --complexation
 
-    > python -m arrow.test.test_arrow --plot
+    > python -m stochastic_arrow.test.test_arrow --plot
 
-    > python -m arrow.test.test_arrow --obsidian
+    > python -m stochastic_arrow.test.test_arrow --obsidian
 
-    > python -m arrow.test.test_arrow --memory
+    > python -m stochastic_arrow.test.test_arrow --memory
 
-    > python -m arrow.test.test_arrow --time
+    > python -m stochastic_arrow.test.test_arrow --time
 
 More examples:
 
-    > python -m arrow.test.test_hang
+    > python -m stochastic_arrow.test.test_hang
 
-    > pytest -m arrow/test/test_arrow.py
+    > pytest -m stochastic_arrow/test/test_arrow.py
 
     > pytest -k flagella
 
 ## Changelog
 
+### Version 1.0.0
+
+* Rename module to `stochastic_arrow` to avoid name conflict (Issue #51). **All users must update their import statements to use `stochastic_arrow` instead of `arrow`.**
+
 ### Version 0.5.2
 
 * Update to Cython 0.29.34. (Cython 3.0.0 is now in beta.)

setup.py

@@ -13,11 +13,11 @@
 _ = setuptools
 
 
-with open("README.md", 'r') as readme:
+with open("README.md", 'r', encoding="utf-8") as readme:
     long_description = readme.read()
 
 current_dir = os.getcwd()
-arrow_dir = os.path.join(current_dir, 'arrow')
+arrow_dir = os.path.join(current_dir, 'stochastic_arrow')
 
 # Compile the Cython code to C for development builds:
 #    USE_CYTHON=1 python setup.py build_ext --inplace
@@ -30,25 +30,28 @@
 ext = '.pyx' if USE_CYTHON else '.c'
 
 cython_extensions = [
-    Extension('arrow.arrowhead',
-              sources=['arrow/mersenne.c', 'arrow/obsidian.c', 'arrow/arrowhead'+ext,],
-              include_dirs=['arrow', np.get_include()],
+    Extension('stochastic_arrow.arrowhead',
+              sources=[
+                  'stochastic_arrow/mersenne.c',
+                  'stochastic_arrow/obsidian.c',
+                  'stochastic_arrow/arrowhead'+ext,],
+              include_dirs=['stochastic_arrow', np.get_include()],
               define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
               )]
 
 if USE_CYTHON:
     from Cython.Build import cythonize
     cython_extensions = cythonize(
         cython_extensions,
-        include_path=['arrow'],
+        include_path=['stochastic_arrow'],
         annotate=True,  # to get an HTML code listing
     )
 
 setup(
     name='stochastic-arrow',
-    version='0.5.2',
-    packages=['arrow'],
-    author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst',
+    version='1.0.0',
+    packages=['stochastic_arrow'],
+    author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst, Sean Cheah',
     author_email='[email protected]',
     url='https://github.com/CovertLab/arrow',
     license='MIT',

arrow/analysis/distributions.py → stochastic_arrow/analysis/distributions.py

@@ -96,7 +96,7 @@ def _last_where(bool_array):
 if __name__ == '__main__':
     import matplotlib.pyplot as plt
 
-    from arrow.analysis.plotting import plot_full_history
+    from stochastic_arrow.analysis.plotting import plot_full_history
 
     (fig, axes) = plt.subplots(constrained_layout = True)
 

arrow/arrow.pxd → stochastic_arrow/arrow.pxd

@@ -1,4 +1,4 @@
 # cython: language_level=3str
 
 # This file works around a Cython 3.0.0a1+ error on arrowhead.pyx:
-#    arrow/arrowhead.pyx:14:0: 'arrow.pxd' not found
+#    stochastic_arrow/arrowhead.pyx:14:0: 'arrow.pxd' not found

arrow/arrow.py → stochastic_arrow/arrow.py

@@ -33,9 +33,9 @@ def flat_indexes(assorted_lists):
 
     lengths = np.array([
         len(l)
-        for l in assorted_lists])
-    indexes = np.insert(lengths, 0, 0).cumsum()[:-1]
-    flat = np.array(flatten(assorted_lists))
+        for l in assorted_lists], dtype=np.int64)
+    indexes = np.insert(lengths, 0, 0).cumsum()[:-1].astype(np.int64)
+    flat = np.array(flatten(assorted_lists), dtype=np.int64)
     return flat, lengths, indexes
 
 def reenact_events(stoichiometry, events, state):

arrow/arrowhead.pyx → stochastic_arrow/arrowhead.pyx

@@ -65,8 +65,8 @@ cdef class Arrowhead:
         self.random_seed = random_seed
         mersenne.seed(self.info.random_state, random_seed)
 
-        self.info.reactions_count = stoichiometry.shape[0]
-        self.info.substrates_count = stoichiometry.shape[1]
+        self.info.reactions_count = <int>stoichiometry.shape[0]
+        self.info.substrates_count = <int>stoichiometry.shape[1]
         self.info.stoichiometry = &stoichiometry[0, 0]
 
         self.info.reactants_lengths = &reactants_lengths[0]

arrow/obsidian.c → stochastic_arrow/obsidian.c

@@ -115,14 +115,14 @@ evolve_result evolve(Info *info, double duration, int64_t *state, double *rates)
 
   // if something goes wrong (like an overflow in propensities), the status will be
   // set to some meaningful number
-  int64_t status = 0;
+  int status = 0;
 
   if (time == NULL ||
       events == NULL ||
       outcome == NULL ||
       propensities == NULL ||
       update == NULL) {
-    printf("arrow.obsidian.evolve - failed to allocate memory: %d", errno);
+    printf("stochastic_arrow.obsidian.evolve - failed to allocate memory: %d", errno);
 
     free(time);
     free(events);
@@ -187,14 +187,14 @@ evolve_result evolve(Info *info, double duration, int64_t *state, double *rates)
 
     if (isnan(total)) {
       printf("failed simulation: total propensity is NaN\n");
-      int max_reaction = 0;
+      int64_t max_reaction = 0;
       for (reaction = 0; reaction < reactions_count; reaction++) {
-        printf("reaction %lld is %f\n", reaction, propensities[reaction]);
+        printf("reaction %lld is %f\n", (long long)reaction, propensities[reaction]);
         if (isnan(propensities[reaction]) || propensities[reaction] > propensities[max_reaction]) {
           max_reaction = reaction;
         }
       }
-      printf("largest reaction is %d at %f\n", max_reaction, propensities[max_reaction]);
+      printf("largest reaction is %lld at %f\n", (long long)max_reaction, propensities[max_reaction]);
       interval = 0.0;
       choice = -1;
       status = 1; // overflow
@@ -278,7 +278,7 @@ evolve_result evolve(Info *info, double duration, int64_t *state, double *rates)
       if (step >= event_bounds) {
         double *new_time = malloc((sizeof (double)) * event_bounds * 2);
         if (new_time == NULL) {
-          printf("arrow.obsidian.evolve - failed to allocate memory: %d", errno);
+          printf("stochastic_arrow.obsidian.evolve - failed to allocate memory: %d", errno);
 
           free(time);
           free(events);
@@ -295,7 +295,7 @@ evolve_result evolve(Info *info, double duration, int64_t *state, double *rates)
 
         int64_t *new_events = malloc((sizeof (int64_t)) * event_bounds * 2);
         if (new_events == NULL) {
-          printf("arrow.obsidian.evolve - failed to allocate memory: %d", errno);
+          printf("stochastic_arrow.obsidian.evolve - failed to allocate memory: %d", errno);
 
           free(time);
           free(events);

arrow/reference.py → stochastic_arrow/reference.py

@@ -3,7 +3,7 @@
 import numpy as np
 from six import moves
 
-from arrow.math import multichoose
+from stochastic_arrow.math import multichoose
 
 
 def derive_reactants(stoichiometric_matrix):

arrow/test/negative_counts.py → stochastic_arrow/test/negative_counts.py

@@ -1,6 +1,6 @@
 import json
 
-from arrow import StochasticSystem
+from stochastic_arrow import StochasticSystem
 import numpy as np