From c97c6f8880118ba7e9f8be6570fc760c165a80fb Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 02:26:15 -0800
Subject: [PATCH 01/18] Python 2 compatibility

---
 setup.py                            |  8 ++++++--
 stochastic_arrow/test/test_arrow.py | 18 ++++++++++--------
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/setup.py b/setup.py
index 3f06677..fc40ce4 100644
--- a/setup.py
+++ b/setup.py
@@ -8,13 +8,17 @@
 import setuptools  # used indirectly for bdist_wheel cmd and long_description_content_type
 from distutils.core import setup
 from distutils.extension import Extension
+import sys
 import numpy as np
 
 _ = setuptools
 
 
-with open("README.md", 'r', encoding="utf-8") as readme:
-    long_description = readme.read()
+with open("README.md", 'r') as readme:
+    if sys.version_info[0] < 3:
+        long_description = readme.read().decode('utf-8')
+    else:
+        long_description = readme.read()
 
 current_dir = os.getcwd()
 arrow_dir = os.path.join(current_dir, 'stochastic_arrow')
diff --git a/stochastic_arrow/test/test_arrow.py b/stochastic_arrow/test/test_arrow.py
index d97284b..db14eae 100644
--- a/stochastic_arrow/test/test_arrow.py
+++ b/stochastic_arrow/test/test_arrow.py
@@ -15,7 +15,6 @@
 from time import time as seconds_since_epoch
 import json
 import numpy as np
-from pathlib import Path
 import platform
 import psutil
 import pytest
@@ -296,12 +295,15 @@ def test_fail_flagella():
 
 # All reaction propensities should be printed if simulation fails
 def test_fail_stdout():
-    curr_file = Path(os.path.realpath(__file__))
-    main_dir = curr_file.parents[2]
+    curr_file = os.path.realpath(__file__)
+    main_dir = os.path.dirname(os.path.dirname(os.path.dirname(curr_file)))
     # sys.executable more reliable than 'python' in Windows virtualenv
-    result = subprocess.run(
+    env = os.environ.copy()
+    env.update({'PYTHONPATH': str(main_dir)})
+    result = subprocess.Popen(
         [sys.executable, curr_file, '--test-fail-flagella'],
-        capture_output=True, env={**os.environ, 'PYTHONPATH': str(main_dir)})
+        stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env)
+    stdout, stderr = result.communicate()
     assert re.search((
         'failed simulation: total propensity is NaN.*'
         'reaction 0 is -?0.000000.*'
@@ -311,8 +313,8 @@ def test_fail_stdout():
         'reaction 4 is -?0.000000.*'
         'reaction 5 is -?nan.*'
         'largest reaction is 5 at -?nan.*'),
-        result.stdout.decode('utf-8'), flags=re.DOTALL)
-    assert result.stderr == b''
+        stdout.decode('utf-8'), flags=re.DOTALL)
+    assert stderr == b''
 
 def test_get_set_random_state():
     stoich = np.array([[1, 1, -1, 0], [-2, 0, 0, 1], [-1, -1, 1, 0]],
@@ -398,7 +400,7 @@ def check_gillespie_reference():
         all_axes = np.asarray(all_axes)
 
         for (axes, system) in moves.zip(all_axes.flatten(), systems):
-            print(f'Running {system.__name__}')
+            print('Running {}'.format(system.__name__))
             axes.set_title(system.__name__)
 
             time, counts, events = system()

From 1f3db37c76e36f2eb4d62c3f0bc341755c5c0310 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 02:32:20 -0800
Subject: [PATCH 02/18] Use setuptools and build

---
 Makefile         |  6 ++----
 pyproject.toml   |  3 +++
 requirements.txt |  1 +
 setup.py         | 22 ++++++----------------
 4 files changed, 12 insertions(+), 20 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/Makefile b/Makefile
index 41f5961..6171f2c 100644
--- a/Makefile
+++ b/Makefile
@@ -9,9 +9,7 @@ clean:
 	find . -name "__pycache__" -delete
 
 compile:
-	USE_CYTHON=1 python setup.py build_ext --inplace
+	USE_CYTHON=1 python -m pip install -e .
 
 dist:
-	### bdist_wheel is disabled on linux since the distribution machinery doesn't
-	### yet have a way to specify compatible linux distros.
-	USE_CYTHON=1 python setup.py sdist # bdist_wheel
+	USE_CYTHON=1 python -m build --sdist
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..efa310c
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel", "cython", "numpy"]
+build-backend = "setuptools.build_meta"
diff --git a/requirements.txt b/requirements.txt
index 0c0af41..1c09869 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,6 +2,7 @@
 
 pip
 setuptools
+build
 
 Cython>=0.29.34
 numpy
diff --git a/setup.py b/setup.py
index fc40ce4..6f60fe5 100644
--- a/setup.py
+++ b/setup.py
@@ -1,17 +1,8 @@
-# distutils is deprecated; to be removed for Python 3.12.
-# See https://numpy.org/devdocs/reference/distutils_status_migration.html for
-# migration advice.
-# This setup.py file no longer uses numpy.distutils so it might be easy to
-# move fully to setuptools.
-
 import os
-import setuptools  # used indirectly for bdist_wheel cmd and long_description_content_type
-from distutils.core import setup
-from distutils.extension import Extension
+from setuptools import Extension, setup
 import sys
 import numpy as np
 
-_ = setuptools
 
 
 with open("README.md", 'r') as readme:
@@ -24,9 +15,9 @@
 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
+#    USE_CYTHON=1 python -m pip install -e .
 # and for building source distribution packages:
-#    USE_CYTHON=1 python setup.py sdist
+#    USE_CYTHON=1 python -m build --sdist
 # and *not* when installing a distribution package.
 # See http://docs.cython.org/en/latest/src/userguide/source_files_and_compilation.html#distributing-cython-modules
 USE_CYTHON = 'USE_CYTHON' in os.environ
@@ -39,7 +30,7 @@
                   'stochastic_arrow/mersenne.c',
                   'stochastic_arrow/obsidian.c',
                   'stochastic_arrow/arrowhead'+ext,],
-              include_dirs=['stochastic_arrow', np.get_include()],
+              include_dirs=[arrow_dir, np.get_include()],
               define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
               )]
 
@@ -47,7 +38,7 @@
     from Cython.Build import cythonize
     cython_extensions = cythonize(
         cython_extensions,
-        include_path=['stochastic_arrow'],
+        include_path=[arrow_dir],
         annotate=True,  # to get an HTML code listing
     )
 
@@ -59,11 +50,10 @@
     author_email='ryan.spangler@gmail.com',
     url='https://github.com/CovertLab/arrow',
     license='MIT',
-    include_dirs=[arrow_dir, np.get_include()],
     ext_modules=cython_extensions,
     long_description=long_description,
     long_description_content_type='text/markdown',
-    requires=['numpy (>=1.14)', 'six'],
+    install_requires=['numpy>=1.14', 'six'],
     classifiers=[
         'Development Status :: 3 - Alpha',
         'License :: OSI Approved :: MIT License',

From 2468066075112d002a520accc106f84c8dfb9632 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 02:32:56 -0800
Subject: [PATCH 03/18] Test cibuildwheel

---
 .github/workflows/release.yml | 154 ++++++++++++++++++++++++++++++++++
 1 file changed, 154 insertions(+)
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..3acb3c5
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,154 @@
+name: Build and upload to PyPI
+
+on:
+  push:
+    branches:
+      - master
+      - numpy2
+  release:
+    types:
+      - published
+
+jobs:
+  # Build the wheels for Linux, Windows and macOS for Python 3.9 and newer
+  build_wheels:
+    name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+      matrix:
+        include:
+          # Window 64 bit
+          - os: windows-latest
+            python: 39
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 310
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 311
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 312
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 313
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 313t
+            platform_id: win_amd64
+            free_threaded_support: True
+
+          # Linux 64 bit manylinux2014
+          - os: ubuntu-latest
+            python: 39
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 310
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 311
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 312
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 313
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 313t
+            platform_id: manylinux_x86_64
+            free_threaded_support: True
+
+          # MacOS x86_64
+          - os: macos-13
+            python: 39
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 310
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 311
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 312
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 313
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 313t
+            platform_id: macosx_x86_64
+            free_threaded_support: True
+
+          # MacOS arm64
+          - os: macos-14
+            python: 39
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 310
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 311
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 312
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 313
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 313t
+            platform_id: macosx_arm64
+            free_threaded_support: True
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        env:
+          CIBW_FREE_THREADED_SUPPORT: ${{ matrix.free_threaded_support }}
+          CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
+          CIBW_TEST_REQUIRES: pytest psutil
+          CIBW_TEST_COMMAND: pytest {package}/test
+          USE_CYTHON: 1
+        uses: pypa/cibuildwheel@v2.22.0
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

From 92a308a7bf6aaabc321ac202d4dc4eebaaf236d9 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 04:04:20 -0800
Subject: [PATCH 04/18] Fix Windows decoding

---
 setup.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index 6f60fe5..52c73b9 100644
--- a/setup.py
+++ b/setup.py
@@ -3,12 +3,11 @@
 import sys
 import numpy as np
 
-
-
-with open("README.md", 'r') as readme:
-    if sys.version_info[0] < 3:
+if sys.version_info[0] < 3:
+    with open("README.md", 'r') as readme:
         long_description = readme.read().decode('utf-8')
-    else:
+else:
+    with open("README.md", 'r', encoding="utf-8") as readme:
         long_description = readme.read()
 
 current_dir = os.getcwd()

From 9cfc7f939c976247e44fe12518199d8ece91ea5c Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 04:06:29 -0800
Subject: [PATCH 05/18] Fix paths

---
 setup.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index 52c73b9..ccbb463 100644
--- a/setup.py
+++ b/setup.py
@@ -10,9 +10,6 @@
     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, 'stochastic_arrow')
-
 # Compile the Cython code to C for development builds:
 #    USE_CYTHON=1 python -m pip install -e .
 # and for building source distribution packages:
@@ -29,7 +26,7 @@
                   'stochastic_arrow/mersenne.c',
                   'stochastic_arrow/obsidian.c',
                   'stochastic_arrow/arrowhead'+ext,],
-              include_dirs=[arrow_dir, np.get_include()],
+              include_dirs=['stochastic_arrow', np.get_include()],
               define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
               )]
 
@@ -37,7 +34,7 @@
     from Cython.Build import cythonize
     cython_extensions = cythonize(
         cython_extensions,
-        include_path=[arrow_dir],
+        include_path=['stochastic_arrow'],
         annotate=True,  # to get an HTML code listing
     )
 

From 70a8c408bcae1682a881962ca1578f093b877c66 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 04:18:11 -0800
Subject: [PATCH 06/18] Set USE_CYTHON to 1 in wheel builds

---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 3acb3c5..f4c4450 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -112,7 +112,7 @@ jobs:
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           CIBW_TEST_REQUIRES: pytest psutil
           CIBW_TEST_COMMAND: pytest {package}/test
-          USE_CYTHON: 1
+          CIBW_ENVIRONMENT: USE_CYTHON=1
         uses: pypa/cibuildwheel@v2.22.0
 
       - uses: actions/upload-artifact@v4

From 6601b277403c2054b931dd7b3c76777fbd303181 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 04:20:13 -0800
Subject: [PATCH 07/18] Fix test directory

---
 .github/workflows/release.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f4c4450..a35a30d 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -111,7 +111,9 @@ jobs:
           CIBW_FREE_THREADED_SUPPORT: ${{ matrix.free_threaded_support }}
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           CIBW_TEST_REQUIRES: pytest psutil
-          CIBW_TEST_COMMAND: pytest {package}/test
+          CIBW_TEST_COMMAND: |
+            cp -r {project}/stochastic_arrow/test tmp_test_dir/
+            pytest tmp_test_dir
           CIBW_ENVIRONMENT: USE_CYTHON=1
         uses: pypa/cibuildwheel@v2.22.0
 

From 30e8606f7dfd2ff919bf7862db426fc968cb6d02 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 04:50:56 -0800
Subject: [PATCH 08/18] Fix pytests and install pre-release Cython for
 free-threading support

---
 .github/workflows/release.yml | 7 +++++--
 pyproject.toml                | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index a35a30d..a6e148b 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -112,8 +112,11 @@ jobs:
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           CIBW_TEST_REQUIRES: pytest psutil
           CIBW_TEST_COMMAND: |
-            cp -r {project}/stochastic_arrow/test tmp_test_dir/
-            pytest tmp_test_dir
+            mkdir tmp_test_dir
+            cp -r {project}/stochastic_arrow/test tmp_test_dir/test
+            cp -r {project}/data tmp_test_dir/data
+            cd tmp_test_dir
+            pytest
           CIBW_ENVIRONMENT: USE_CYTHON=1
         uses: pypa/cibuildwheel@v2.22.0
 
diff --git a/pyproject.toml b/pyproject.toml
index efa310c..c34e725 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools", "wheel", "cython", "numpy"]
+requires = ["setuptools", "wheel", "cython==3.1.0a1; python_version=='3.13'", "cython; python_version!='3.13'", "numpy"]
 build-backend = "setuptools.build_meta"

From c05b4066b7db3457f33acaa44c9b7e6582a64222 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 05:11:38 -0800
Subject: [PATCH 09/18] Try marking freethreading compatible

---
 stochastic_arrow/arrow.pxd     | 1 +
 stochastic_arrow/arrowhead.pyx | 1 +
 stochastic_arrow/mersenne.pxd  | 1 +
 stochastic_arrow/obsidian.pxd  | 1 +
 4 files changed, 4 insertions(+)

diff --git a/stochastic_arrow/arrow.pxd b/stochastic_arrow/arrow.pxd
index a5b4559..172af76 100644
--- a/stochastic_arrow/arrow.pxd
+++ b/stochastic_arrow/arrow.pxd
@@ -1,4 +1,5 @@
 # cython: language_level=3str
+# cython: freethreading_compatible = True
 
 # This file works around a Cython 3.0.0a1+ error on arrowhead.pyx:
 #    stochastic_arrow/arrowhead.pyx:14:0: 'arrow.pxd' not found
diff --git a/stochastic_arrow/arrowhead.pyx b/stochastic_arrow/arrowhead.pyx
index ddd0e94..902680c 100644
--- a/stochastic_arrow/arrowhead.pyx
+++ b/stochastic_arrow/arrowhead.pyx
@@ -1,4 +1,5 @@
 # cython: language_level=3str
+# cython: freethreading_compatible = True
 
 from __future__ import absolute_import, division, print_function
 
diff --git a/stochastic_arrow/mersenne.pxd b/stochastic_arrow/mersenne.pxd
index 5e70d0a..94f4d05 100644
--- a/stochastic_arrow/mersenne.pxd
+++ b/stochastic_arrow/mersenne.pxd
@@ -1,4 +1,5 @@
 # cython: language_level=3str
+# cython: freethreading_compatible = True
 
 from libc.stdint cimport uint32_t
 
diff --git a/stochastic_arrow/obsidian.pxd b/stochastic_arrow/obsidian.pxd
index 16981df..ea5a943 100644
--- a/stochastic_arrow/obsidian.pxd
+++ b/stochastic_arrow/obsidian.pxd
@@ -1,4 +1,5 @@
 # cython: language_level=3str
+# cython: freethreading_compatible = True
 
 from libc.stdint cimport int64_t, uint32_t
 

From 93af1c8222188a366a0537651a9e1d6ab34f39e9 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 05:13:21 -0800
Subject: [PATCH 10/18] Ignore memory increases on macOS

---
 stochastic_arrow/test/test_arrow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochastic_arrow/test/test_arrow.py b/stochastic_arrow/test/test_arrow.py
index db14eae..245682c 100644
--- a/stochastic_arrow/test/test_arrow.py
+++ b/stochastic_arrow/test/test_arrow.py
@@ -224,7 +224,7 @@ def test_memory():
 
     print('obsidian C implementation elapsed seconds for {} runs: {}'.format(
         amplify, obsidian_end - obsidian_start))
-    if platform.system() == 'Windows':
+    if platform.system() == 'Windows' or platform.system() == 'Darwin':
         assert memory_increases <= 10
     else:
         assert memory_increases <= 1

From 088d8ab81f652d16ebb5ecc98bb30651f65e0be8 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 12:06:29 -0800
Subject: [PATCH 11/18] Fix Windows test command

---
 .github/workflows/release.yml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index a6e148b..dfbbb5b 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -2,9 +2,6 @@ name: Build and upload to PyPI
 
 on:
   push:
-    branches:
-      - master
-      - numpy2
   release:
     types:
       - published
@@ -117,6 +114,16 @@ jobs:
             cp -r {project}/data tmp_test_dir/data
             cd tmp_test_dir
             pytest
+          CIBW_TEST_COMMAND_WINDOWS: |
+            echo "Starting tests on Windows";
+            mkdir tmp_test_dir;
+            echo "Copying test directory";
+            xcopy /E /I /Y stochastic_arrow\test tmp_test_dir\test;
+            echo "Copying data directory";
+            xcopy /E /I /Y stochastic_arrow\data tmp_test_dir\data;
+            cd tmp_test_dir;
+            echo "Running pytest on Windows";
+            pytest -v
           CIBW_ENVIRONMENT: USE_CYTHON=1
         uses: pypa/cibuildwheel@v2.22.0
 

From b6c46a1809ca53528e49f866c8b7f837bae62226 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 13:52:55 -0800
Subject: [PATCH 12/18] Test publish

---
 .github/workflows/release.yml | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index dfbbb5b..f197b46 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -149,10 +149,30 @@ jobs:
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
-    environment: pypi
+    environment:
+      name: pypi
+      url: https://pypi.org/p/stochastic-arrow
     permissions:
       id-token: write
     if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+  
+  upload_pypi_test:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/stochastic-arrow
+    permissions:
+      id-token: write
     steps:
       - uses: actions/download-artifact@v4
         with:

From b2f25fd8644d9f1f4d3b43a8cf44098bde655b77 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 15:26:06 -0800
Subject: [PATCH 13/18] Reorganize code into src folder to avoid import issues

---
 .github/workflows/release.yml                  |  17 +----------------
 .gitignore                                     |   6 +++---
 MANIFEST.in                                    |   4 ++--
 Makefile                                       |   4 +++-
 .../analysis => analysis}/__init__.py          |   0
 .../analysis => analysis}/distributions.py     |   0
 .../analysis => analysis}/plotting.py          |   0
 setup.py                                       |  17 ++++++++++-------
 .../stochastic_arrow}/__init__.py              |   0
 .../stochastic_arrow}/arrow.pxd                |   0
 .../stochastic_arrow}/arrow.py                 |   0
 .../stochastic_arrow}/arrowhead.pyx            |   0
 .../stochastic_arrow}/math.py                  |   0
 .../stochastic_arrow}/mersenne.c               |   0
 .../stochastic_arrow}/mersenne.h               |   0
 .../stochastic_arrow}/mersenne.pxd             |   0
 .../stochastic_arrow}/obsidian.c               |   0
 .../stochastic_arrow}/obsidian.h               |   0
 .../stochastic_arrow}/obsidian.pxd             |   0
 .../stochastic_arrow}/reference.py             |   0
 {stochastic_arrow/test => test}/__init__.py    |   0
 .../test => test}/complex-counts.npy           | Bin
 .../test => test}/negative_counts.py           |   0
 {stochastic_arrow/test => test}/rates.npy      | Bin
 {stochastic_arrow/test => test}/stoich.npy     | Bin
 {stochastic_arrow/test => test}/test_arrow.py  |   0
 {stochastic_arrow/test => test}/test_hang.py   |   0
 27 files changed, 19 insertions(+), 29 deletions(-)
 rename {stochastic_arrow/analysis => analysis}/__init__.py (100%)
 rename {stochastic_arrow/analysis => analysis}/distributions.py (100%)
 rename {stochastic_arrow/analysis => analysis}/plotting.py (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/__init__.py (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/arrow.pxd (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/arrow.py (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/arrowhead.pyx (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/math.py (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/mersenne.c (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/mersenne.h (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/mersenne.pxd (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/obsidian.c (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/obsidian.h (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/obsidian.pxd (100%)
 rename {stochastic_arrow => src/stochastic_arrow}/reference.py (100%)
 rename {stochastic_arrow/test => test}/__init__.py (100%)
 rename {stochastic_arrow/test => test}/complex-counts.npy (100%)
 rename {stochastic_arrow/test => test}/negative_counts.py (100%)
 rename {stochastic_arrow/test => test}/rates.npy (100%)
 rename {stochastic_arrow/test => test}/stoich.npy (100%)
 rename {stochastic_arrow/test => test}/test_arrow.py (100%)
 rename {stochastic_arrow/test => test}/test_hang.py (100%)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f197b46..d72bd3a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -108,22 +108,7 @@ jobs:
           CIBW_FREE_THREADED_SUPPORT: ${{ matrix.free_threaded_support }}
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           CIBW_TEST_REQUIRES: pytest psutil
-          CIBW_TEST_COMMAND: |
-            mkdir tmp_test_dir
-            cp -r {project}/stochastic_arrow/test tmp_test_dir/test
-            cp -r {project}/data tmp_test_dir/data
-            cd tmp_test_dir
-            pytest
-          CIBW_TEST_COMMAND_WINDOWS: |
-            echo "Starting tests on Windows";
-            mkdir tmp_test_dir;
-            echo "Copying test directory";
-            xcopy /E /I /Y stochastic_arrow\test tmp_test_dir\test;
-            echo "Copying data directory";
-            xcopy /E /I /Y stochastic_arrow\data tmp_test_dir\data;
-            cd tmp_test_dir;
-            echo "Running pytest on Windows";
-            pytest -v
+          CIBW_TEST_COMMAND: pytest -v {project}/test
           CIBW_ENVIRONMENT: USE_CYTHON=1
         uses: pypa/cibuildwheel@v2.22.0
 
diff --git a/.gitignore b/.gitignore
index 5352095..4fa54bf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,9 +10,9 @@ profile
 /.idea/
 /tmp/
 
-stochastic_arrow/arrowhead.c
-stochastic_arrow/arrowhead.*.pyd
-stochastic_arrow/*.html
+src/stochastic_arrow/arrowhead.c
+src/stochastic_arrow/arrowhead.*.pyd
+src/stochastic_arrow/*.html
 
 arrow.egg-info/
 stochastic_arrow.egg-info/
diff --git a/MANIFEST.in b/MANIFEST.in
index 1f4aaf8..2c1e001 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,2 @@
-include stochastic_arrow/obsidian.h
-include stochastic_arrow/mersenne.h
\ No newline at end of file
+include src/stochastic_arrow/obsidian.h
+include src/stochastic_arrow/mersenne.h
\ No newline at end of file
diff --git a/Makefile b/Makefile
index 6171f2c..49cdf4e 100644
--- a/Makefile
+++ b/Makefile
@@ -2,9 +2,11 @@
 .DEFAULT_GOAL := compile
 
 clean:
-	### Files for older versions of stochastic_arrow are in arrow folder
+	### Files for older versions of stochastic_arrow are in arrow or stochastic_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/
+	### Newer versions of stochastic_arrow are in src/stochastic_arrow folder
+	rm -rf src/stochastic_arrow/arrowhead*.so src/stochastic_arrow/arrowhead.c src/stochastic_arrow/arrowhead.html src/stochastic_arrow.egg-info/
 	find . -name "*.pyc" -delete
 	find . -name "__pycache__" -delete
 
diff --git a/stochastic_arrow/analysis/__init__.py b/analysis/__init__.py
similarity index 100%
rename from stochastic_arrow/analysis/__init__.py
rename to analysis/__init__.py
diff --git a/stochastic_arrow/analysis/distributions.py b/analysis/distributions.py
similarity index 100%
rename from stochastic_arrow/analysis/distributions.py
rename to analysis/distributions.py
diff --git a/stochastic_arrow/analysis/plotting.py b/analysis/plotting.py
similarity index 100%
rename from stochastic_arrow/analysis/plotting.py
rename to analysis/plotting.py
diff --git a/setup.py b/setup.py
index ccbb463..0d554dd 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
 import os
-from setuptools import Extension, setup
+from setuptools import Extension, find_packages, setup
 import sys
 import numpy as np
 
@@ -20,13 +20,15 @@
 
 ext = '.pyx' if USE_CYTHON else '.c'
 
+arrow_dir = os.path.join('src', 'stochastic_arrow')
+
 cython_extensions = [
     Extension('stochastic_arrow.arrowhead',
               sources=[
-                  'stochastic_arrow/mersenne.c',
-                  'stochastic_arrow/obsidian.c',
-                  'stochastic_arrow/arrowhead'+ext,],
-              include_dirs=['stochastic_arrow', np.get_include()],
+                  os.path.join(arrow_dir, 'mersenne.c'),
+                  os.path.join(arrow_dir, 'obsidian.c'),
+                  os.path.join(arrow_dir, 'arrowhead'+ext),],
+              include_dirs=[arrow_dir, np.get_include()],
               define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
               )]
 
@@ -34,14 +36,15 @@
     from Cython.Build import cythonize
     cython_extensions = cythonize(
         cython_extensions,
-        include_path=['stochastic_arrow'],
+        include_path=[arrow_dir],
         annotate=True,  # to get an HTML code listing
     )
 
 setup(
     name='stochastic-arrow',
     version='1.0.0',
-    packages=['stochastic_arrow'],
+    packages=find_packages('src'),
+    package_dir={'': 'src'},
     author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst, Sean Cheah',
     author_email='ryan.spangler@gmail.com',
     url='https://github.com/CovertLab/arrow',
diff --git a/stochastic_arrow/__init__.py b/src/stochastic_arrow/__init__.py
similarity index 100%
rename from stochastic_arrow/__init__.py
rename to src/stochastic_arrow/__init__.py
diff --git a/stochastic_arrow/arrow.pxd b/src/stochastic_arrow/arrow.pxd
similarity index 100%
rename from stochastic_arrow/arrow.pxd
rename to src/stochastic_arrow/arrow.pxd
diff --git a/stochastic_arrow/arrow.py b/src/stochastic_arrow/arrow.py
similarity index 100%
rename from stochastic_arrow/arrow.py
rename to src/stochastic_arrow/arrow.py
diff --git a/stochastic_arrow/arrowhead.pyx b/src/stochastic_arrow/arrowhead.pyx
similarity index 100%
rename from stochastic_arrow/arrowhead.pyx
rename to src/stochastic_arrow/arrowhead.pyx
diff --git a/stochastic_arrow/math.py b/src/stochastic_arrow/math.py
similarity index 100%
rename from stochastic_arrow/math.py
rename to src/stochastic_arrow/math.py
diff --git a/stochastic_arrow/mersenne.c b/src/stochastic_arrow/mersenne.c
similarity index 100%
rename from stochastic_arrow/mersenne.c
rename to src/stochastic_arrow/mersenne.c
diff --git a/stochastic_arrow/mersenne.h b/src/stochastic_arrow/mersenne.h
similarity index 100%
rename from stochastic_arrow/mersenne.h
rename to src/stochastic_arrow/mersenne.h
diff --git a/stochastic_arrow/mersenne.pxd b/src/stochastic_arrow/mersenne.pxd
similarity index 100%
rename from stochastic_arrow/mersenne.pxd
rename to src/stochastic_arrow/mersenne.pxd
diff --git a/stochastic_arrow/obsidian.c b/src/stochastic_arrow/obsidian.c
similarity index 100%
rename from stochastic_arrow/obsidian.c
rename to src/stochastic_arrow/obsidian.c
diff --git a/stochastic_arrow/obsidian.h b/src/stochastic_arrow/obsidian.h
similarity index 100%
rename from stochastic_arrow/obsidian.h
rename to src/stochastic_arrow/obsidian.h
diff --git a/stochastic_arrow/obsidian.pxd b/src/stochastic_arrow/obsidian.pxd
similarity index 100%
rename from stochastic_arrow/obsidian.pxd
rename to src/stochastic_arrow/obsidian.pxd
diff --git a/stochastic_arrow/reference.py b/src/stochastic_arrow/reference.py
similarity index 100%
rename from stochastic_arrow/reference.py
rename to src/stochastic_arrow/reference.py
diff --git a/stochastic_arrow/test/__init__.py b/test/__init__.py
similarity index 100%
rename from stochastic_arrow/test/__init__.py
rename to test/__init__.py
diff --git a/stochastic_arrow/test/complex-counts.npy b/test/complex-counts.npy
similarity index 100%
rename from stochastic_arrow/test/complex-counts.npy
rename to test/complex-counts.npy
diff --git a/stochastic_arrow/test/negative_counts.py b/test/negative_counts.py
similarity index 100%
rename from stochastic_arrow/test/negative_counts.py
rename to test/negative_counts.py
diff --git a/stochastic_arrow/test/rates.npy b/test/rates.npy
similarity index 100%
rename from stochastic_arrow/test/rates.npy
rename to test/rates.npy
diff --git a/stochastic_arrow/test/stoich.npy b/test/stoich.npy
similarity index 100%
rename from stochastic_arrow/test/stoich.npy
rename to test/stoich.npy
diff --git a/stochastic_arrow/test/test_arrow.py b/test/test_arrow.py
similarity index 100%
rename from stochastic_arrow/test/test_arrow.py
rename to test/test_arrow.py
diff --git a/stochastic_arrow/test/test_hang.py b/test/test_hang.py
similarity index 100%
rename from stochastic_arrow/test/test_hang.py
rename to test/test_hang.py

From b793f568239e6b3b66c5c72365665bcdc9a3a7e6 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 15:37:45 -0800
Subject: [PATCH 14/18] Fix data dir for pytest

---
 {data => test/data}/complexation/beginning-final.json   | 0
 {data => test/data}/complexation/beginning-initial.json | 0
 {data => test/data}/complexation/large-initial.json     | 0
 {data => test/data}/complexation/simple-final.json      | 0
 {data => test/data}/complexation/simple-initial.json    | 0
 {data => test/data}/complexation/stoichiometry.json     | 0
 test/negative_counts.py                                 | 6 +++++-
 test/test_arrow.py                                      | 2 +-
 8 files changed, 6 insertions(+), 2 deletions(-)
 rename {data => test/data}/complexation/beginning-final.json (100%)
 rename {data => test/data}/complexation/beginning-initial.json (100%)
 rename {data => test/data}/complexation/large-initial.json (100%)
 rename {data => test/data}/complexation/simple-final.json (100%)
 rename {data => test/data}/complexation/simple-initial.json (100%)
 rename {data => test/data}/complexation/stoichiometry.json (100%)

diff --git a/data/complexation/beginning-final.json b/test/data/complexation/beginning-final.json
similarity index 100%
rename from data/complexation/beginning-final.json
rename to test/data/complexation/beginning-final.json
diff --git a/data/complexation/beginning-initial.json b/test/data/complexation/beginning-initial.json
similarity index 100%
rename from data/complexation/beginning-initial.json
rename to test/data/complexation/beginning-initial.json
diff --git a/data/complexation/large-initial.json b/test/data/complexation/large-initial.json
similarity index 100%
rename from data/complexation/large-initial.json
rename to test/data/complexation/large-initial.json
diff --git a/data/complexation/simple-final.json b/test/data/complexation/simple-final.json
similarity index 100%
rename from data/complexation/simple-final.json
rename to test/data/complexation/simple-final.json
diff --git a/data/complexation/simple-initial.json b/test/data/complexation/simple-initial.json
similarity index 100%
rename from data/complexation/simple-initial.json
rename to test/data/complexation/simple-initial.json
diff --git a/data/complexation/stoichiometry.json b/test/data/complexation/stoichiometry.json
similarity index 100%
rename from data/complexation/stoichiometry.json
rename to test/data/complexation/stoichiometry.json
diff --git a/test/negative_counts.py b/test/negative_counts.py
index 6f2209f..5a314ee 100644
--- a/test/negative_counts.py
+++ b/test/negative_counts.py
@@ -1,4 +1,5 @@
 import json
+import os
 
 from stochastic_arrow import StochasticSystem
 import numpy as np
@@ -6,7 +7,10 @@
 
 duration = 2**31
 
-with open('data/complexation/large-initial.json') as f:
+# Build the path to the data file relative to the script's directory
+data_path = os.path.join(os.path.dirname(__file__), 'data', 'complexation', 'large-initial.json')
+
+with open(data_path) as f:
     data = json.load(f)
 
 stoich = np.array(data['stoich'])
diff --git a/test/test_arrow.py b/test/test_arrow.py
index 245682c..918e583 100644
--- a/test/test_arrow.py
+++ b/test/test_arrow.py
@@ -84,7 +84,7 @@ def test_dimerization():
 
 
 def load_complexation(prefix='simple'):
-    fixtures_root = os.path.join('data', 'complexation')
+    fixtures_root = os.path.join(os.path.dirname(__file__), 'data', 'complexation')
 
     def load_state(filename):
         with open(os.path.join(fixtures_root, filename)) as f:

From 3589de18424953375a05a9e4416d8077168d9393 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Thu, 5 Dec 2024 15:48:09 -0800
Subject: [PATCH 15/18] v1.1.0

---
 README.md | 5 +++++
 setup.py  | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 7885bb9..1f6ce05 100644
--- a/README.md
+++ b/README.md
@@ -122,6 +122,11 @@ More examples:
 
 ## Changelog
 
+### Version 1.1.0
+* Update build toolchain and automatically build/publish wheels for all
+major platforms and recent Python versions.
+* Build wheels with Numpy 2+ support
+
 ### 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`.**
diff --git a/setup.py b/setup.py
index 0d554dd..2706347 100644
--- a/setup.py
+++ b/setup.py
@@ -42,7 +42,7 @@
 
 setup(
     name='stochastic-arrow',
-    version='1.0.0',
+    version='1.1.0',
     packages=find_packages('src'),
     package_dir={'': 'src'},
     author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst, Sean Cheah',

From 8a8c67a81dce0d361d5424d711d07da003e1be96 Mon Sep 17 00:00:00 2001
From: Jerry Morrison <1fish2@users.noreply.github.com>
Date: Fri, 6 Dec 2024 22:50:23 -0800
Subject: [PATCH 16/18] Fix the CLI test runner

* Fix the clunky CLI test runner.
  * Update the README about it.
  * The `--plot` test requires installing matplotlib, in particular, one that's compatible with the installed numpy.
  * Moved the `analysis/` directory into the `test/` directory for the tests to import.
  * TODO: Fix the `--memory` test, which fails `assert memory_increases <= 10` on macOS.
  * TODO: Fix the `--plot` test, which raises `ValueError: x and y must have same first dimension, but have shapes (115,) and (114, 2469)` from matplotlib.
* Delete `release.sh` which would be risky to run now and has been supplanted by GitHub Actions. Actually my process was to copy/paste from this script rather than run it as is.

Q. Do *.pxd header files need `freethreading_compatible = True` or is it sufficient in the .pyx module?
---
 Makefile                                     |  3 ++
 README.md                                    | 37 ++++++++++-----
 optional_requirements.txt                    |  2 +-
 release.sh                                   | 50 --------------------
 {analysis => test/analysis}/__init__.py      |  0
 {analysis => test/analysis}/distributions.py |  2 +-
 {analysis => test/analysis}/plotting.py      |  0
 test/test_arrow.py                           |  7 +--
 8 files changed, 33 insertions(+), 68 deletions(-)
 delete mode 100755 release.sh
 rename {analysis => test/analysis}/__init__.py (100%)
 rename {analysis => test/analysis}/distributions.py (97%)
 rename {analysis => test/analysis}/plotting.py (100%)

diff --git a/Makefile b/Makefile
index 49cdf4e..67deef3 100644
--- a/Makefile
+++ b/Makefile
@@ -13,5 +13,8 @@ clean:
 compile:
 	USE_CYTHON=1 python -m pip install -e .
 
+test: clean compile
+	pytest test
+
 dist:
 	USE_CYTHON=1 python -m build --sdist
diff --git a/README.md b/README.md
index 1f6ce05..1cdd3eb 100644
--- a/README.md
+++ b/README.md
@@ -91,32 +91,43 @@ from stochastic_arrow import reenact_events
 history = reenact_events(stoichiometric_matrix, result['events'], state)
 ```
 
-## Testing
-
-`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
+## Building
 
     > make clean compile
-    > pytest
+
+This builds the extension package and installs it in editable mode.
 
 **NOTE:** `make compile` without an explicit `clean` might not fully build the extension.
 
-There are more command line features in test_arrow:
+## Testing
 
-    > python -m stochastic_arrow.test.test_arrow --complexation
+`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/).
+To run the main tests, in the source tree:
 
-    > python -m stochastic_arrow.test.test_arrow --plot
+    > make test
 
-    > python -m stochastic_arrow.test.test_arrow --obsidian
+or
 
-    > python -m stochastic_arrow.test.test_arrow --memory
+    > pytest
 
-    > python -m stochastic_arrow.test.test_arrow --time
+There are additional command line features in test_arrow:
 
-More examples:
+    > python -m test.test_arrow --help
+    > python -m test.test_arrow --complexation
+    > python -m test.test_arrow --complexation --runs 3
+    > python -m test.test_arrow --obsidian
+    > python -m test.test_arrow --memory
+    > python -m test.test_arrow --time
+    > python -m test.test_arrow --pickle
+    > python -m test.test_arrow --test-fail-flagella
+    > python -m test.test_arrow --test-fail-stdout
+    > python -m test.test_hang
 
-    > python -m stochastic_arrow.test.test_hang
+This test requires installing a version of matplotlib that's compatible with the installed numpy:
 
-    > pytest -m stochastic_arrow/test/test_arrow.py
+    > python -m test.test_arrow --plot
+
+More examples:
 
     > pytest -k flagella
 
diff --git a/optional_requirements.txt b/optional_requirements.txt
index ae9e316..6ccafc3 100644
--- a/optional_requirements.txt
+++ b/optional_requirements.txt
@@ -1 +1 @@
-matplotlib==2.2.3
+matplotlib
diff --git a/release.sh b/release.sh
deleted file mode 100755
index b7d9cad..0000000
--- a/release.sh
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/bin/bash
-# Build a new release including a git tag and and publish it to PyPI.
-# Do some basic checks to avoid mistakes.
-#
-# Usage: ./release.sh 0.1.0
-
-set -eu
-
-version=$1
-
-# Check the version number.
-setup_py_version="$(python setup.py --version)"
-if [ "$setup_py_version" != "$version" ]; then
-    echo "setup.py has version `$setup_py_version`, not `$version`."
-    echo "Aborting."
-    exit 1
-fi
-
-# Check that the working directory is clean.
-if [ ! -z "$(git status --untracked-files=no --porcelain)" ]; then
-    echo "You have uncommitted git changes."
-    echo "Aborting."
-    exit 1
-fi
-
-# Check that we are on master.
-branch="$(git rev-parse --abbrev-ref HEAD)"
-if [ "$branch" != "master" ]; then
-    echo "You are on git branch `$branch` but should release from `master`."
-    echo "Aborting."
-    exit 1
-fi
-
-# Create and push a git tag.
-git tag -m "Version v$version" "v$version"
-git push --tags
-
-# Compile and test, allowing test failures.
-make clean compile
-set +e
-pytest
-set -e
-
-# Create and publish the package.
-rm -rf dist build *.egg-info
-python setup.py sdist
-twine upload dist/*
-
-echo "Version v$version has been published on PyPI and has a git tag."
-echo "Please make a GitHub Release from that tag."
diff --git a/analysis/__init__.py b/test/analysis/__init__.py
similarity index 100%
rename from analysis/__init__.py
rename to test/analysis/__init__.py
diff --git a/analysis/distributions.py b/test/analysis/distributions.py
similarity index 97%
rename from analysis/distributions.py
rename to test/analysis/distributions.py
index c7eaf02..b430f6c 100644
--- a/analysis/distributions.py
+++ b/test/analysis/distributions.py
@@ -96,7 +96,7 @@ def _last_where(bool_array):
 if __name__ == '__main__':
     import matplotlib.pyplot as plt
 
-    from stochastic_arrow.analysis.plotting import plot_full_history
+    from .plotting import plot_full_history
 
     (fig, axes) = plt.subplots(constrained_layout = True)
 
diff --git a/analysis/plotting.py b/test/analysis/plotting.py
similarity index 100%
rename from analysis/plotting.py
rename to test/analysis/plotting.py
diff --git a/test/test_arrow.py b/test/test_arrow.py
index 918e583..ffc00f4 100644
--- a/test/test_arrow.py
+++ b/test/test_arrow.py
@@ -378,7 +378,7 @@ def check_gillespie_reference():
                 system()
     else:
         import matplotlib.pyplot as plt
-        from stochastic_arrow.analysis.plotting import plot_full_history
+        from .analysis.plotting import plot_full_history
 
         n_systems = len(systems)
 
@@ -412,9 +412,10 @@ def check_gillespie_reference():
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(
-        description='Run one of these tests')
+        description='Run the specified test or some default tests')
     parser.add_argument('--complexation', action='store_true')
-    parser.add_argument('--runs', type=int, default=1)
+    parser.add_argument('--runs', type=int, default=1,
+        help='an option for complexation')
     parser.add_argument('--plot', action='store_true')
     parser.add_argument('--obsidian', action='store_true')
     parser.add_argument('--memory', action='store_true')

From 059538585fe876c9707d454f228dcbcf72f9f777 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Sun, 8 Dec 2024 01:09:08 -0800
Subject: [PATCH 17/18] Remove unnecessary Cython directives

---
 src/stochastic_arrow/arrow.pxd    | 5 +----
 src/stochastic_arrow/mersenne.pxd | 3 ---
 src/stochastic_arrow/obsidian.pxd | 3 ---
 3 files changed, 1 insertion(+), 10 deletions(-)

diff --git a/src/stochastic_arrow/arrow.pxd b/src/stochastic_arrow/arrow.pxd
index 172af76..2d8bce5 100644
--- a/src/stochastic_arrow/arrow.pxd
+++ b/src/stochastic_arrow/arrow.pxd
@@ -1,5 +1,2 @@
-# cython: language_level=3str
-# cython: freethreading_compatible = True
-
-# This file works around a Cython 3.0.0a1+ error on arrowhead.pyx:
+# This file works around a Cython 3.0.0a1 error on arrowhead.pyx:
 #    stochastic_arrow/arrowhead.pyx:14:0: 'arrow.pxd' not found
diff --git a/src/stochastic_arrow/mersenne.pxd b/src/stochastic_arrow/mersenne.pxd
index 94f4d05..c9e24cb 100644
--- a/src/stochastic_arrow/mersenne.pxd
+++ b/src/stochastic_arrow/mersenne.pxd
@@ -1,6 +1,3 @@
-# cython: language_level=3str
-# cython: freethreading_compatible = True
-
 from libc.stdint cimport uint32_t
 
 
diff --git a/src/stochastic_arrow/obsidian.pxd b/src/stochastic_arrow/obsidian.pxd
index ea5a943..612bfb4 100644
--- a/src/stochastic_arrow/obsidian.pxd
+++ b/src/stochastic_arrow/obsidian.pxd
@@ -1,6 +1,3 @@
-# cython: language_level=3str
-# cython: freethreading_compatible = True
-
 from libc.stdint cimport int64_t, uint32_t
 
 from mersenne cimport MTState

From 5fc79dbe9ab890fb81120e9444b2e5f91a78c51c Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Wed, 11 Dec 2024 16:59:03 -0800
Subject: [PATCH 18/18] Remove TestPyPI CI job

---
 .github/workflows/release.yml | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index d72bd3a..d89c5ca 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -149,23 +149,3 @@ jobs:
           merge-multiple: true
 
       - uses: pypa/gh-action-pypi-publish@release/v1
-  
-  upload_pypi_test:
-    needs: [build_wheels, build_sdist]
-    runs-on: ubuntu-latest
-    environment:
-      name: testpypi
-      url: https://test.pypi.org/p/stochastic-arrow
-    permissions:
-      id-token: write
-    steps:
-      - uses: actions/download-artifact@v4
-        with:
-          # unpacks all CIBW artifacts into dist/
-          pattern: cibw-*
-          path: dist
-          merge-multiple: true
-
-      - uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          repository-url: https://test.pypi.org/legacy/