Merge branch 'main' of https://github.com/USEPA/pybeepop

.github/workflows/build-beepop.yml

@@ -13,6 +13,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: quanted/vpoplib
+          ref: dev
       - name: Build BeePop+
         run: |
           mkdir build
@@ -25,4 +26,4 @@ jobs:
           name: compiled-${{ matrix.os }}
           path: |
             build/*.so
-            build/Release/*.dll
+            build/Release/*.dll

.github/workflows/ci-build-publish.yml

@@ -0,0 +1,109 @@
+name: CI-Build-Publish
+
+on:
+    push:
+      branches:
+        - main
+      paths:
+        - pybeepop/**
+        - .github/workflows/ci-build-publish.yml
+        - pyproject.toml
+        - build.py
+      #    tags:        
+  #      - '*.*.*'
+    pull_request:
+    release:
+    workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Checkout BeePop+ code
+        uses: actions/checkout@v4
+        with:
+            repository: quanted/vpoplib
+            ref: dev
+            path: beepop
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: auto64
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+        with:
+          config-file: "pyproject.toml"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ 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 poetry build --format=sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_testpypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: 
+      name: testpypi
+      url: https://test.pypi.org/p/pybeepop-plus
+    permissions:
+      id-token: write
+    # if: github.event_name == 'release' && github.event.action == 'created'
+    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    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/
+          skip-existing: true
+
+  upload_pypi:
+      needs: [build_wheels, build_sdist]
+      runs-on: ubuntu-latest
+      environment: 
+        name: pypi
+        url: https://pypi.org/p/pybeepop-plus
+      permissions:
+        id-token: write
+      if: github.event_name == 'release' && github.event.action == 'published'
+      # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+      # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+      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:
+            skip-existing: true

.github/workflows/run-tests-ubuntu.yml

@@ -1,6 +1,7 @@
 name: Run PyTests on Ubuntu
 
-on: [push, pull_request]
+#on: [push, pull_request]
+on: workflow_dispatch
 
 jobs:
   build:
@@ -11,7 +12,7 @@ jobs:
         python-version: ["3.x"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:

README.md

@@ -31,7 +31,7 @@ for Linux are [below](#compiling-beepop-on-linux). Source code is available on [
 
 1. **Install the package** into your Python environment using pip:
 
-        pip install git+https://github.com/usepa/pybeepop.git
+        pip install pybeepop-plus
         
 2.  **Import the PyBeePop class** in your python code, e.g.:
 

build.py

@@ -0,0 +1,2 @@
+def build(setup_kwargs):
+    print("Placehold build code!")

paper/paper.md

@@ -21,7 +21,7 @@ bibliography: paper.bib
 
 Honey bees (*Apis mellifera* L.) provide critical pollination services
 for both natural and agricultural systems, with $50 billion USD of crops
-completely dependent on pollination in the United Statates alone [@reilly:2020]. However, honey bees are facing a wide 
+completely dependent on pollination in the United States alone [@reilly:2020]. However, honey bees are facing a wide 
 range of stressors resulting in elevated colony failure rates including
 climate change [@zapata:2024], pathogens [@evans:2011], habitat loss and 
 decreased food availability [@donkersley:2014; @goulson:2015], and exposure to 

pybeepop/pybeepop.py

@@ -46,17 +46,18 @@ def __init__(
             if self.platform == "Windows":
                 if platform.architecture()[0] == "32bit":
                     raise NotImplementedError(
-                        "Windows x86 (32 bit) is not supported by BeePop+. Please run on an x64 platform."
+                        "Windows x86 (32-bit) is not supported by BeePop+. Please run on an x64 platform."
                     )
                 else:
                     lib_file = os.path.join(self.parent, "lib/beepop_win64.dll")
             elif self.platform == "Linux":
-                lib_file = os.path.join(self.parent, "lib/beepop_ubuntu.so")  # try ubuntu
+                lib_file = os.path.join(self.parent, "lib/beepop_linux.so")
                 if self.verbose:
                     print(
                         """
-                        Running in Linux mode. Trying Ubuntu pre-compiled BeePop+.
-                        You may need to compile your own version of BeePop+ from source and pass the path to your .so file with the lib_file option.
+                        Running in Linux mode. Trying manylinux/musllinux version.
+                        If you encounter errors, you may need to compile your own version of BeePop+ from source and pass the path to your
+                        .so file with the lib_file option. Currently, only 64-bit architecture is supported.
                         See the pybeepop README for instructions.
                         """
                     )
@@ -67,6 +68,7 @@ def __init__(
                 """
                 BeePop+ shared object library does not exist or is not compatible with your operating system. 
                 You may need to compile BeePop+ from source (see https://github.com/USEPA/pybeepop/blob/main/README.md for more info.)
+                Currently, only 64-bit architecture is supported.
                 """
             )
         self.lib_file = lib_file

pybeepop/tools.py

@@ -237,7 +237,7 @@ def run_beepop(self):
             self.lib.ClearResultsBuffer()
             out_lines = []
             for j in range(0, n_result_lines - 1):
-                out_lines.append(p_Results[j].decode("utf-8", errors="replace"))
+                out_lines.append(p_Results[j].decode("utf-8", errors="strict"))
             out_str = io.StringIO("\n".join(out_lines))
             out_df = pd.read_csv(
                 out_str, sep="\\s+", skiprows=3, names=colnames, dtype={"Date": str}

pybeepop_example.ipynb

@@ -64,7 +64,9 @@
    "id": "668d00a5",
    "metadata": {},
    "source": [
-    "### Set parameters, load example weather, parameter, and pesticide residue files"
+    "### Set parameters, load example weather, parameter, and pesticide residue files\n",
+    "\n",
+    "Example files are available on the project [GitHub page](https://github.com/USEPA/pybeepop/tree/main/example_data)."
    ]
   },
   {

pyproject.toml

@@ -1,9 +1,12 @@
 [tool.poetry]
 name = "pybeepop-plus"
-version = "0.1.0"
+version = "0.1.1"
 description = "EPA's Python wrapper for the EPA/USDA honey bee colony model BeePop+"
 authors = ["Jeffrey Minucci <[email protected]>"]
+maintainers = ["Jeffrey Minucci <[email protected]>"]
+license = "MIT"
 readme = "README.md"
+repository = "https://github.com/USEPA/pybeepop"
 documentation = "https://usepa.github.io/pybeepop/"
 packages = [
     { include = "pybeepop", from ="." },
@@ -13,12 +16,53 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python",
+    "Intended Audience :: Science/Research",
 ]
 
 [tool.poetry.dependencies]
-python = "^3.9.0"
+python = "^3.8.0"
 pandas = "^2.0.0"
 
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core", "setuptools"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.build]
+script = "build.py"
+generate-setup-file = true
+
+[tool.cibuildwheel.linux]
+before-all = ["yum -y install cmake",
+    "cd beepop",
+    "mkdir build",
+    "cd build",
+    "cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON ..",
+    "cmake --build . --config Release",
+    "pwd",
+    "cp liblibvpop.so ../../pybeepop/lib",
+    "mv -f ../../pybeepop/lib/liblibvpop.so ../../pybeepop/lib/beepop_linux.so",
+]
+
+[tool.cibuildwheel.windows]
+before-all = [
+    "cd beepop",
+    "mkdir build",
+    "cd build",
+    "cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON ..",
+    "cmake --build . --config Release",
+    "copy Release\\libvpop.dll ..\\..\\pybeepop\\lib",
+    "move /y ..\\..\\pybeepop\\lib\\libvpop.dll ..\\..\\pybeepop\\lib\\beepop_win64.dll",
+]
+
+[[tool.cibuildwheel.overrides]]
+select = "*-musllinux*"
+before-all = ["apk add cmake",
+    "cd beepop",
+    "mkdir build",
+    "cd build",
+    "cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON ..",
+    "cmake --build . --config Release",
+    "pwd",
+    "cp liblibvpop.so ../../pybeepop/lib",
+    "mv -f ../../pybeepop/lib/liblibvpop.so ../../pybeepop/lib/beepop_linux.so",
+]

tests/test_pybeepop.py

@@ -9,7 +9,8 @@
 
 
 def test_set_parameters():
-    beepop = PyBeePop()
+    beepop = PyBeePop(verbose=True)
+    print(beepop.lib_file)
     test_parameters = {"ICWorkerAdults": 9999, "SimStart": "01/01/2020", "SimEnd": "10/31/2020"}
     beepop.set_parameters(test_parameters)
     params = beepop.get_parameters()
@@ -42,7 +43,8 @@ def test_invalid_parameter_in_file():
 
 
 def test_run_model():
-    beepop = PyBeePop()
+    beepop = PyBeePop(verbose=True)
+    print(beepop.lib_file)
 
     # Define inputs and file paths
     START_DATE = "06/16/2014"
@@ -68,6 +70,8 @@ def test_run_model():
 
     # run model
     results = beepop.run_model()
+    print(results)
+    print(len(results))
     results_initial = results.iloc[0, :]
     results_last = results.iloc[len(results) - 1, :]
     results_exposure = results.iloc[20, :]
@@ -78,9 +82,9 @@ def test_run_model():
     assert results_initial["Capped Worker Brood"] == 8000
     assert results_exposure["Colony Size"] == 17913
     assert results_exposure["Capped Drone Brood"] == 219
-    assert results_exposure["Daylight hours"] == 13.7
+    assert round(results_exposure["Daylight hours"],1) == 13.7
     assert results_exposure["Dead Foragers"] == 155
-    assert results_last["Date"] == "10/9/2014"
+    assert results_last["Date"] == "10/09/2014"
     assert results_last["Colony Size"] == 43932
     assert results_last["Adult Drones"] == 512
     assert results_last["Average Temperature (C)"] == 16.66