Merge pull request #99 from cropsinsilico/topic/cppseri_migration

Topic/cppseri migration
cropsinsilico · Jun 27, 2023 · ae9bd57 · ae9bd57
2 parents 70705bb + 67ed4a4
commit ae9bd57
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diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml
@@ -264,6 +264,12 @@ jobs:
 
         echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV
 
+        '
+      shell: bash -l {0}
+    - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, '--suite=examples')
+      name: (WINDOWS) Disable interpreted language example on Windows for speed
+      run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV
+
         '
       shell: bash -l {0}
     - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC
@@ -309,11 +315,18 @@ jobs:
         restore-keys: '${{ runner.os }}-pip-
 
           '
-    - if: matrix.install-method == 'pip'
+    - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os
+        != 'macOS')
       name: (PIP) Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os
+        == 'macOS'
+      name: (PIP) Set up Python 3.7
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.7.16
     - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
       name: (PIP) Set up Julia
       uses: julia-actions/setup-julia@v1
@@ -431,12 +444,13 @@ jobs:
       id: test1
       name: Run tests (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }}
+        }} ${{ env.TEST_FLAGS1_SUFFIX }}
       timeout-minutes: 120
     - if: ${{ steps.test1.outcome == 'failure' }}
       name: Re-run test failures (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }} --last-failed --last-failed-no-failures=all --second-attempt
+        }} ${{ env.TEST_FLAGS1_SUFFIX }} --last-failed --last-failed-no-failures=all
+        --second-attempt
       timeout-minutes: 120
     - continue-on-error: true
       id: test1_script
@@ -597,6 +611,12 @@ jobs:
 
         echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV
 
+        '
+      shell: bash -l {0}
+    - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, '--suite=examples')
+      name: (WINDOWS) Disable interpreted language example on Windows for speed
+      run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV
+
         '
       shell: bash -l {0}
     - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC
@@ -642,11 +662,18 @@ jobs:
         restore-keys: '${{ runner.os }}-pip-
 
           '
-    - if: matrix.install-method == 'pip'
+    - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os
+        != 'macOS')
       name: (PIP) Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os
+        == 'macOS'
+      name: (PIP) Set up Python 3.7
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.7.16
     - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
       name: (PIP) Set up Julia
       uses: julia-actions/setup-julia@v1
@@ -764,12 +791,13 @@ jobs:
       id: test1
       name: Run tests (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }}
+        }} ${{ env.TEST_FLAGS1_SUFFIX }}
       timeout-minutes: 120
     - if: ${{ steps.test1.outcome == 'failure' }}
       name: Re-run test failures (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }} --last-failed --last-failed-no-failures=all --second-attempt
+        }} ${{ env.TEST_FLAGS1_SUFFIX }} --last-failed --last-failed-no-failures=all
+        --second-attempt
       timeout-minutes: 120
     - continue-on-error: true
       id: test1_script
@@ -922,6 +950,12 @@ jobs:
 
         echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV
 
+        '
+      shell: bash -l {0}
+    - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, '--suite=examples')
+      name: (WINDOWS) Disable interpreted language example on Windows for speed
+      run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV
+
         '
       shell: bash -l {0}
     - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC
@@ -967,11 +1001,18 @@ jobs:
         restore-keys: '${{ runner.os }}-pip-
 
           '
-    - if: matrix.install-method == 'pip'
+    - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os
+        != 'macOS')
       name: (PIP) Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os
+        == 'macOS'
+      name: (PIP) Set up Python 3.7
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.7.16
     - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
       name: (PIP) Set up Julia
       uses: julia-actions/setup-julia@v1
@@ -1089,12 +1130,13 @@ jobs:
       id: test1
       name: Run tests (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }}
+        }} ${{ env.TEST_FLAGS1_SUFFIX }}
       timeout-minutes: 120
     - if: ${{ steps.test1.outcome == 'failure' }}
       name: Re-run test failures (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }} --last-failed --last-failed-no-failures=all --second-attempt
+        }} ${{ env.TEST_FLAGS1_SUFFIX }} --last-failed --last-failed-no-failures=all
+        --second-attempt
       timeout-minutes: 120
     - continue-on-error: true
       id: test1_script
@@ -1230,6 +1272,12 @@ jobs:
 
         echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV
 
+        '
+      shell: bash -l {0}
+    - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, '--suite=examples')
+      name: (WINDOWS) Disable interpreted language example on Windows for speed
+      run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV
+
         '
       shell: bash -l {0}
     - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC
@@ -1275,11 +1323,18 @@ jobs:
         restore-keys: '${{ runner.os }}-pip-
 
           '
-    - if: matrix.install-method == 'pip'
+    - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os
+        != 'macOS')
       name: (PIP) Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os
+        == 'macOS'
+      name: (PIP) Set up Python 3.7
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.7.16
     - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
       name: (PIP) Set up Julia
       uses: julia-actions/setup-julia@v1
@@ -1397,12 +1452,13 @@ jobs:
       id: test1
       name: Run tests (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }}
+        }} ${{ env.TEST_FLAGS1_SUFFIX }}
       timeout-minutes: 120
     - if: ${{ steps.test1.outcome == 'failure' }}
       name: Re-run test failures (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }} --last-failed --last-failed-no-failures=all --second-attempt
+        }} ${{ env.TEST_FLAGS1_SUFFIX }} --last-failed --last-failed-no-failures=all
+        --second-attempt
       timeout-minutes: 120
     - continue-on-error: true
       id: test1_script
@@ -1537,6 +1593,12 @@ jobs:
 
         echo "TEMP=$USERPROFILE\\AppData\\Local\\Temp" >> $GITHUB_ENV
 
+        '
+      shell: bash -l {0}
+    - if: runner.os == 'Windows' && startsWith(matrix.test-flags1, '--suite=examples')
+      name: (WINDOWS) Disable interpreted language example on Windows for speed
+      run: 'echo "TEST_FLAGS1_SUFFIX=--skip-languages python R julia" >> $GITHUB_ENV
+
         '
       shell: bash -l {0}
     - if: runner.os == 'Windows' && matrix.install-method == 'pip' && env.INSTALLC
@@ -1582,11 +1644,18 @@ jobs:
         restore-keys: '${{ runner.os }}-pip-
 
           '
-    - if: matrix.install-method == 'pip'
+    - if: matrix.install-method == 'pip' && (matrix.python-version != 3.7 || runner.os
+        != 'macOS')
       name: (PIP) Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && matrix.python-version == 3.7 && runner.os
+        == 'macOS'
+      name: (PIP) Set up Python 3.7
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.7.16
     - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
       name: (PIP) Set up Julia
       uses: julia-actions/setup-julia@v1
@@ -1704,12 +1773,13 @@ jobs:
       id: test1
       name: Run tests (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }}
+        }} ${{ env.TEST_FLAGS1_SUFFIX }}
       timeout-minutes: 120
     - if: ${{ steps.test1.outcome == 'failure' }}
       name: Re-run test failures (1st)
       run: pytest --import-mode=importlib --ci --cov-append ${{ matrix.test-flags1
-        }} --last-failed --last-failed-no-failures=all --second-attempt
+        }} ${{ env.TEST_FLAGS1_SUFFIX }} --last-failed --last-failed-no-failures=all
+        --second-attempt
       timeout-minutes: 120
     - continue-on-error: true
       id: test1_script

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,18 @@
 History
 =======
 
+1.10.1 (2023-06-27) New map transformation, composite function wrapping example, and various refactoring of internal methods
+-------------------
+
+* Added map transformation for converting arrays into map types
+* Added support for automatted wrapping of C++ model functions that have arguments with types of std::string, std::vector, or std::map.
+* Added composite_function example of wrapping multiple inputs of different types to a function as separate channels and composite_function2 example of wrapping multiple inputs & outputs to a function as single channels
+* Added 'count' FileComm parameter to specify the number of times a file should be read
+* Refactor geometry serialization classes to use rapidjson methods
+* Refactor how additional variables created during function wrapping are handled
+* Updated C++ interface to use updated rapidjson that requires allocators for yggdrasil types
+* Allow use of with_asan with CMake/Make models
+
 1.10.0 (2023-05-31) Added support for PyTorch models, sequence files, image files, and Excel files
 -------------------
 

diff --git a/_vendor/python_rapidjson/CHANGES.rst b/_vendor/python_rapidjson/CHANGES.rst
@@ -1,6 +1,22 @@
 Changes
 -------
 
+1.10 (2023-03-15)
+~~~~~~~~~~~~~~~~~
+
+* Use `current master`__ version of rapidjson
+
+  __ https://github.com/Tencent/rapidjson/commit/083f359f5c36198accc2b9360ce1e32a333231d9
+
+* Produce ppc64le wheels, thanks to mgiessing (`PR #170`__)
+
+  __ https://github.com/python-rapidjson/python-rapidjson/pull/170
+
+* Use cibuildwheel `2.21.1`__
+
+  __ https://cibuildwheel.readthedocs.io/en/stable/changelog/#v2121
+
+
 1.9 (2022-10-17)
 ~~~~~~~~~~~~~~~~