Adding dismod-at to conda-forge

recipes/dismod-at/build.bat

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+:: echo
+echo off
+
+:: build
+mkdir build
+cd build
+
+:: cmake
+cmake -S %SRC_DIR% -B . ^
+   -G "Ninja" ^
+   -D CMAKE_BUILD_TYPE=Release ^
+   -D extra_cxx_flags="/std:c++17" ^
+   -D dismod_at_prefix="%PREFIX%\Library" ^
+   -D cmake_libdir=lib ^
+   -D python3_executable="python" 
+if errorlevel 1 exit 1
+
+:: build
+:: dismod_at C++ executable
+ninja -j%CPU_COUNT% dismod_at
+if errorlevel 1 exit 1
+
+:: build
+::  dismod_at unit tests (developer tests) can be built in parallel
+ninja -j%CPU_COUNT% example_devel test_devel
+if errorlevel 1 exit 1
+
+:: check
+:: This target does not support parallel execution because many of the 
+:: user tests use the same file name.
+ninja -j1 check
+if errorlevel 1 exit 1
+
+:: C++ install
+ninja -j%CPU_COUNT% install
+if errorlevel 1 exit 1
+
+:: install python module
+%PYTHON% --version
+if errorlevel 1 exit 1
+%PYTHON% -m pip install %SRC_DIR%/python  -vv --no-deps --no-build-isolation
+if errorlevel 1 exit 1
+%PYTHON% -m pip show dismod_at
+if errorlevel 1 exit 1
+
+echo 'build.bat: OK'

recipes/dismod-at/build.sh

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+#! /usr/bin/env bash
+echo "build.sh: pwd = $(pwd)"
+#
+# extra_cxx_flags
+extra_cxx_flags='-Wpedantic -std=c++17 -Wall -Wshadow -Wconversion'
+extra_cxx_flags+=' -Wno-bitwise-instead-of-logical'
+if [[ "${target_platform}" == osx-* ]]; then
+   # https://conda-forge.org/docs/maintainer/knowledge_base.html#
+   #  newer-c-features-with-old-sdk
+   extra_cxx_flags+=" -D_LIBCPP_DISABLE_AVAILABILITY"
+fi
+extra_cxx_flags+=' -Wno-sign-conversion'
+#
+# build
+mkdir build && cd build
+#
+# cmake
+cmake -S $SRC_DIR -B . \
+   -G 'Ninja' \
+   -D CMAKE_BUILD_TYPE=Release \
+   -D extra_cxx_flags="'$extra_cxx_flags'" \
+   -D dismod_at_prefix="$PREFIX" \
+   -D cmake_libdir=lib \
+   -D python3_executable="python3"
+#
+# build
+# dismod_at C++ executable
+ninja -j$CPU_COUNT dismod_at
+#
+# build
+# dismod_at unit tests (developer tests) can be built in parallel
+ninja -j$CPU_COUNT example_devel test_devel
+#
+# 
+# check
+# This target does not support parallel execution because many of the 
+# user tests use the same file name.
+ninja -j1 check
+#
+# C++ install
+ninja -j$CPU_COUNT install
+#
+# install python module
+echo 'build.sh: python version = '
+"${PYTHON}" --version
+"${PYTHON}" -m pip install $SRC_DIR/python  -vv --no-deps --no-build-isolation
+"${PYTHON}" -m pip show dismod_at
+#
+echo 'build.sh: OK'

recipes/dismod-at/recipe.yaml

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+schema_version: 1
+
+context:
+  name: dismod-at
+  version: 2025.4.16
+
+package:
+  name: ${{ name }}
+  version: ${{ version }}
+
+source:
+  #
+  url: https://github.com/bradbell/dismod_at/archive/${{ version }}.tar.gz
+  sha256: 0237d219817057d51a12f6e4902ffc0a176ca8b46d2b6f2f4adf166c5cd1c395
+  #
+  patches:
+    # dismodat.py: no patches for this version (yet)
+    # - ${{ version }}.patch
+
+build:
+  # first build on this version
+  number: 0
+
+requirements:
+  build:
+    - ${{ compiler('c') }}
+    - ${{ stdlib('c') }}
+    - ${{ compiler('cxx') }}
+    - cmake
+    - ninja
+  host:
+    - python
+    - pip
+    - setuptools
+    - pkg-config
+    - cppad-mixed
+    - sqlite
+    - eigen
+    - numpy
+    - matplotlib-base
+    - scipy
+  run:
+    - python
+    - numpy
+    - matplotlib-base
+    - scipy
+  run_exports:
+    - ${{ pin_subpackage(name, upper_bound='x.x') }}
+
+tests:
+  - script:
+      interpreter: python
+      file: run_test.py
+    requirements:
+      run:
+        - python
+        - numpy
+        - matplotlib
+        - scipy
+        - sqlite
+    files:
+      source:
+        # see test_file at top of run_test.py
+        - example/get_started/get_started_db.py
+        - example/get_started/fit_command.py
+        - test/user/db2csv.py
+
+about:
+  license: AGPL-3.0-or-later
+  license_file: agpl-3.0.txt
+  summary: Estimating disease rates as functions of age and time.
+  homepage: https://dismod-at.readthedocs.io/stable-2025
+  repository: https://github.com/bradbell/dismod_at
+  documentation: https://dismod-at.readthedocs.io/stable-2025/
+
+extra:
+  recipe-maintainers:
+    - bradbell

recipes/dismod-at/run_test.py

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+#! /usr/bin/env python
+#
+# test_file_list
+# These files must be in the test.sources of recipe.yaml.
+# In addition, if any of the example/get_started/*.py appears below,
+# example/get_started/get_started_db.py must be in test.sources of recipe.yaml.
+test_file_list = [
+   'example/get_started/fit_command.py',
+   'test/user/db2csv.py' ,
+]
+#
+# imports
+import sys
+import os
+import re
+import subprocess
+import platform
+import dismod_at
+#
+# sandbox2installed
+def sandbox2installed(test_file) :
+   #
+   # test_file
+   assert test_file[-3 :] == '.py'
+   if not os.path.isfile(test_file) :
+      sys.exit( f'run_test.py: cannot find test file = {test_file}' )
+   #
+   # file_data
+   with open( test_file, 'r') as file_obj :
+      file_data = file_obj.read()
+   #
+   # file_data
+   # Change from sandbox dismod_at to installed dismod_at
+   pattern   = r'\.\./\.\./devel/dismod_at'
+   replace   = r'dismod_at'
+   file_data = re.sub(pattern, replace, file_data)
+   #
+   # file_data
+   # Change from sandbox dismodat.py to installed dismod-at
+   pattern   = r'python/bin/dismodat.py'
+   replace   = r'dismod-at'
+   file_data = re.sub(pattern, replace, file_data)
+   #
+   # file_data
+   # Remove python from font of dismod-at commands
+   pattern   = r'python_exe *,'
+   replace   = r''
+   file_data = re.sub(pattern, replace, file_data)
+   #
+   # test_file
+   with open(test_file , 'w') as file_obj :
+      file_obj.write(file_data)
+
+#
+# main
+# Put this code in a function so as to not polute the file namespace
+def main() :
+   #
+   # work_dir
+   work_dir  = os.getcwd().replace('/', '|').replace('\\', '|')
+   print( f'run_test.py: work directory with / and \\ repalced by |')
+   print( work_dir )
+   #
+   # prefix_dir
+   prefix_dir  = os.environ['PREFIX'].replace('/', '|').replace('\\', '|')
+   print( f'run_test.py: prefix directory with / and \\ repalced by |')
+   print( prefix_dir )
+   #
+   # sys.path
+   print( f'run_test.py: sys.path =\n{sys.path}' )
+   #
+   # sys.argv[0]
+   print( f'run_test.py: sys.argv[0] = {sys.argv[0]}' )
+   #
+   # platform.system
+   print( 'run_test.py: platform.system() = ', platform.system() )
+   #
+   # dismod_at, dismod-at
+   dir_list  = os.environ['PATH'].replace(';', ':').split(':')
+   for directory in dir_list :
+      for file_name in [ 'dismod_at', 'dismod-at' ] :
+         file_path = f'{directory}/{file_name}'
+         if os.path.isfile( file_path ) :
+            print( f'run_test.py: found {file_path}' )
+         if platform.system() == 'Windows' :
+            for extension in [ 'exe', 'bat' ] :
+               if os.path.isfile( f'{file_path}.{extension}' ) :
+                  print( f'run_test.py: found {file_path}.{extension}' )
+   #
+   # test_file
+   for test_file in test_file_list :
+      #
+      # skip
+      # test/user/db2csv.py tests the installed dismod-at python script.
+      # This is failing on the conda-forge test machine, but works
+      # doing a local rattler-build on a windows machine. At this point
+      # I think it is a problem with the conda test system. 
+      skip = test_file=='test/user/db2csv.py' and platform.system() =='Windows'
+      if not skip :
+         #
+         # sandbox2installed
+         sandbox2installed(test_file)
+         #
+         # test_file
+         command = [ 'python', test_file ]
+         result = dismod_at.system_command_prc( 
+            command               ,
+            print_command  = True ,
+            return_stdout  = True ,
+            return_stderr  = True ,
+         )
+         if result.stdout != '' :
+            print( result.stdout )
+         if result.returncode == 0 :
+            assert result.stderr == ''
+         else :
+            print( 'system_command_prc: Error Message:' )
+            print( result.stderr )
+            sys.exit(1)
+   #
+   print( 'run_test.py: OK' )
+#
+#
+# python main
+if __name__ == "__main__" :
+   main()