DO NOT MERGE {main-> niehs}

.Rbuildignore

@@ -1 +1,2 @@
 cran-comments.md
+CHANGELOG.md

.dockerignore

@@ -0,0 +1,10 @@
+.git/
+.github/
+build/
+data/
+inst/
+man/
+R/
+tests/
+tools/
+vignettes/

.github/workflows/dev-enviro.yml

@@ -0,0 +1,32 @@
+name: Developer environment
+
+on:
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.11"]
+        os: [ubuntu-22.04]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip wheel
+          python -m pip install -r requirements_dev.txt
+      - name: Check all Makefile commands
+        run: |
+          make clean
+          make lint
+          make format
+          make test
+          make coverage
+          make build

.github/workflows/python-test-windows.yml

@@ -0,0 +1,95 @@
+name: Python test windows
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+env:
+  PYTHON_LIBRARY_DIR: $Env:CONDA\Lib\site-packages
+  PYTHON_EXECUTABLE: $Env:CONDA\python.exe
+  BUILD_TYPE: Release
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref_name }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.11"]
+        os: ["windows-2022"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: set up python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: set dependency direcory
+        run: echo "DEPENDENCY_DIR=$HOME\github-deps" >> $env:GITHUB_ENV
+      - name: restore github dependencies from cache
+        id: cache-github
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.DEPENDENCY_DIR }}
+          key: ${{runner.os}}-github-deps
+      - name: create dependency dir
+        if: steps.cache-github.outputs.cache-hit != 'true'
+        run: mkdir ${{ env.DEPENDENCY_DIR }}
+      - name: download eigen
+        if: steps.cache-github.outputs.cache-hit != 'true'
+        run: |
+          cd ${{ env.DEPENDENCY_DIR }}
+          git clone --depth 1 https://github.com/libigl/eigen.git
+      - name: install nlopt
+        if: steps.cache-github.outputs.cache-hit != 'true'
+        run: |
+          cd ${{ env.DEPENDENCY_DIR }}
+          git clone --depth 1 https://github.com/stevengj/nlopt.git
+          cd nlopt
+          mkdir build
+          cd build
+          cmake ..
+          cmake --build . --config Release
+      - name: install gsl
+        if: steps.cache-github.outputs.cache-hit != 'true'
+        run: |
+          cd ${{ env.DEPENDENCY_DIR }}
+          git clone --depth 1 https://github.com/ampl/gsl.git
+          cd gsl
+          mkdir build
+          cd build
+          cmake .. -DNO_AMPL_BINDINGS=1
+          cmake --build . --config Release
+      - name: set eigen/nlopt/gsl directories
+        run: |
+          echo "EIGEN_DIR=${{ env.DEPENDENCY_DIR }}\eigen" >> $env:GITHUB_ENV
+          echo "NLOPT_DIR=${{ env.DEPENDENCY_DIR }}\nlopt\src\api;${{ env.DEPENDENCY_DIR }}\nlopt\build\Release;${{ env.DEPENDENCY_DIR }}\nlopt\build" >> $env:GITHUB_ENV
+          echo "GSL_DIR=${{ env.DEPENDENCY_DIR }}\gsl\build\Release;${{ env.DEPENDENCY_DIR }}\gsl\build" >> $env:GITHUB_ENV
+      - name: build bmds with cmake
+        shell: pwsh
+        run: |
+          mkdir build
+          cd build
+          cmake ..
+          cmake --build . --config Release
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip wheel
+          python -m pip install -r requirements_dev.txt
+      - name: Build pybmds
+        run: |
+          python setup.py develop
+          stubgen -p pybmds.bmdscore -o src
+          ruff format src\pybmds\bmdscore.pyi
+          python setup.py bdist_wheel
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./dist/*.whl

.github/workflows/python-test.yml

@@ -0,0 +1,45 @@
+name: Python test linux
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.11"]
+        os: ["ubuntu-22.04"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip wheel
+          python -m pip install -r requirements_dev.txt
+      - name: Check linting
+        run: |
+          make lint
+      - name: Compile bmdscore and build pybmds
+        run: |
+          source ./tools/linux_ci.sh
+          make build
+      - name: Test with pytest
+        run: |
+          make test
+      - name: Build package
+        run: |
+          source ./tools/linux_ci.sh
+          make dist
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./dist/*.whl

.github/workflows/wheels.yml

@@ -0,0 +1,26 @@
+name: Build python packages
+
+on:
+  workflow_dispatch:
+  # push:
+  #   branches:
+  #     - main
+  #   tags:
+
+jobs:
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, windows-2022, macos-12]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: "cp311-* cp312-* *-macosx_arm64 *-win_amd64 *-manylinux_x86_64"
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl

.gitignore

@@ -1,2 +1,31 @@
+*.html
+*.docx
 *.o
+# *.tar.gz
+*.a
+*.la
 *.so
+*.Rproj.user
+*.tgz
+.Rproj.user
+.DS_Store
+*.o
+*.so
+.Rhistory
+build/
+create_dll_compile.bash
+
+# python
+*.egg-info/
+.cache/
+.ipynb_checkpoints/
+.mypy_cache/
+.pytest_cache/
+.vscode/
+dist/
+htmlcov/
+venv/
+*.log
+*.py[cod]
+.coverage
+.env

.gitlab/.gitlab-ci.yml

@@ -0,0 +1,47 @@
+image: python:3.11-slim
+
+stages:
+  - compile
+
+package:
+  stage: compile
+  tags:
+    - devsecops-instance
+  script: |
+    # install
+    apt-get update -y
+    apt-get install -y automake build-essential libtool make cmake libgslcblas0 libgsl-dev
+
+    # build 3rd party
+    cp $CI_PROJECT_DIR/vendor/nlopt-2.7.1.tar.gz ~/nlopt-2.7.1.tar.gz
+    cp $CI_PROJECT_DIR/vendor/eigen-3.4.0.tar.gz ~/eigen-3.4.0.tar.gz
+    # untar
+    cd ~
+    tar -xvf ~/nlopt-2.7.1.tar.gz
+    tar -xvf ~/eigen-3.4.0.tar.gz
+    # build
+    cd ~/nlopt-2.7.1 && mkdir build && cd build && cmake .. && make install
+    cd ~/eigen-3.4.0 && mkdir build && cd build && cmake .. && make install
+    # cleanup
+    cd ~
+    rm -rf nlopt-2.7.1.tar.gz eigen-3.4.0.tar.gz nlopt-2.7.1 eigen-3.4.0
+
+    # build bmds
+    cd $CI_PROJECT_DIR
+    export "LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH"
+    mkdir -p ../BMD_DLL_COMPILE
+    cp ./.gitlab/create_dll_compile.bash.template ./create_dll_compile.bash
+    chmod 700 ./create_dll_compile.bash
+    ./create_dll_compile.bash
+    cd ../BMD_DLL_COMPILE
+    make -j$(nproc)
+    strip --strip-all ./.libs/libDRBMD.so.0.0.0
+
+    # copy
+    mkdir -p $CI_PROJECT_DIR/libs
+    cp ./.libs/* $CI_PROJECT_DIR/libs
+
+  artifacts:
+    paths:
+      - libs/*.so
+

.gitlab/create_dll_compile.bash.template

@@ -0,0 +1,41 @@
+#!/bin/bash
+#Script to copy over the correct R files and then
+#build the correct make scripts using configure.
+
+####################################################
+#ALWAYS NEEDS A PATH TO THE EIGEN DIRECTORY
+#BY DEFAULT IT ASSUMES IT IS IN /usr/local/include/eigen3
+SCRIPT_EIGEN_INCLUDE=/usr/local/include/eigen3
+
+##################################################
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+echo -e "\e[1;31m Assuming Eigen linear algebra library located at \e[0m"
+echo -e "\e[1;32m $SCRIPT_EIGEN_INCLUDE  \e[0m"
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+##################################################
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+echo -e "\e[1;31m Warning removing all information in the directory \e[0m"
+echo -e "\e[1;32m BMD_DLL_COMPILE  \e[0m"
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+echo -e "\e[1;31m ------------------------------------------------\e[0m"
+
+rm -rf ../BMD_DLL_COMPILE
+##############################################################
+mkdir ../BMD_DLL_COMPILE
+mkdir ../BMD_DLL_COMPILE/include
+mkdir ../BMD_DLL_COMPILE/code_base
+cp -a ./src/include/* ../BMD_DLL_COMPILE/include
+cp -a ./src/code_base/* ../BMD_DLL_COMPILE/code_base
+cp ./configure.ac ../BMD_DLL_COMPILE
+cp ./Makefile.am  ../BMD_DLL_COMPILE
+cp ./version.c    ../BMD_DLL_COMPILE
+
+cd ../BMD_DLL_COMPILE
+libtoolize
+aclocal
+autoconf
+automake --add-missing
+./configure --disable-openmp EIGEN_INCLUDE=$SCRIPT_EIGEN_INCLUDE

src/CHANGELOG.md → CHANGELOG.md

@@ -1,6 +1,23 @@
 # Changes
 
-## Version 22.05 (1.0.1)
+## Version 22.8.1.0.2
+
+### The following fixes are in version 1.0.2:
+ 	- Function 'single_continuous_fit' and 'ma_continuous_fit' changed error when defining default priors for
+ 	'distribution=normal-ncv' when data are negative. Originally the variance was described as mean(Y)/var(Y); 
+ 	however, for negative means, this causes NA error. It is now defined as abs(mean(Y))/var(Y). 
+ 	- Log-normal distribution fits were incorrect when summarized data was used. The correct transformation of summarized data is now performed. The formula for standard deviation was typed in as sqrt(log((sd)^2/mu + 1)) it is now sqrt(log((sd/mu)^2+1)). 
+	- Changed default priors for dichotomous fits to be consistant with Wheeler et al. (2020). 
+
+### The following changes to fitting were made: 
+	- Changed MLE Polynomial fit behavior.  Now the terms up to the quadratic are constrained to be in the direction 
+	  of the response.  After this, i.e., degree >= 3, the parameters are unconstrained. 
+
+### Known Problems not yet fixed
+	- GoF for MA individual models not given. 
+	- GoF for dichotomous models with (0/1) data fails. 	
+
+## Version 22.5.1.0.1
 
 ### The following fixes are in version 1.0.1: