Merge branch 'stan-dev:develop' into issue-2783-bernoulli-cdf-stable

Author: andrjohns

.github/CONTRIBUTING.md

@@ -2,8 +2,7 @@
 
 Thanks for reading! We love contributions from everyone in the form of good discussion, issues, and pull requests.
 
-This is the short version. There's more information on the [wiki](https://github.com/stan-dev/math/wiki/Developer-Doc#contributing).
-
+This is the short version. There's more information on the [documentation site](https://mc-stan.org/math/developer_guide.html).
 ## Issues
 
 We reserve [issues](https://github.com/stan-dev/math/issues) for bugs and feature requests that are defined well enough for a developer to tackle. If you have general questions about the Math library, please see the [Discussion](#discussion) section.
@@ -31,22 +30,22 @@ Open feature requests should be the ones we want to implement in the Math librar
 
 ## Pull Requests
 
-All changes to the Math library are handled through [pull requests](https://github.com/stan-dev/math/pulls). Each pull request should correspond to an issue. We follow a [modified GitFlow branching model](https://github.com/stan-dev/stan/wiki/Dev:-Git-Process) for development.
+All changes to the Math library are handled through [pull requests](https://github.com/stan-dev/math/pulls). Each pull request should correspond to an issue. We follow a [modified GitFlow branching model](https://github.com/stan-dev/stan/wiki/Developer-process-overview#2-create-a-branch-for-the-issue) for development.
 
 When a contributor creates a pull request for inclusion to the Math library, here are some of the things we expect:
 
-1. the contribution maintains the Math library's open-source [license](https://github.com/stan-dev/math/wiki/Developer-Doc#licensing): 3-clause BSD
+1. the contribution maintains the Math library's open-source [license](https://github.com/stan-dev/stan/wiki/Stan-Licensing): 3-clause BSD
 2. the code base remains stable after merging the pull request; we expect the `develop` branch to always be in a good state
 3. the changes are maintainable. In code review, we look at the design of the proposed code. We also expect documentation. It should look like idiomatic C++.
 4. the changes are tested. For bugs, we expect at least one test that fails before the patch and is fixed after the patch. For new features, we expect at least one test that shows expected behavior and one test that shows the behavior when there's an error.
-5. the changes adhere to the Math library's [C++ standards](https://github.com/stan-dev/stan/wiki/Code-Quality). Consistency really helps.
+5. the changes adhere to the Math library's [C++ standards](https://github.com/stan-dev/stan/wiki/Coding-Style-and-Idioms). Consistency really helps.
 
 Pull requests are code reviewed after they pass our continuous integration tests. We expect all the above before a pull request is merged. We are an open-source project and once code makes it into the repository, it's on the community to maintain.
 
 It is the responsibility of the contributor submitting the pull request that the code meets these requirements. We're open-source. Once the code gets into the code base, the community of developers take ownership of it.
 
 ### Code Reviews
-See the [Code Review Guidelines](https://github.com/stan-dev/math/wiki/Developer-Doc#code-review-guidelines) on the Math wiki.
+See the [Code Review Guidelines](https://github.com/stan-dev/stan/wiki/Developer-process-overview#code-review-guidelines) on the Math wiki.
 
 
 ## Discussion

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
 Thanks for submitting a pull request! Please remove this text when submitting.
 
-Start by filling in the Summary, Tests, and Side Effects sections of this pull request and then work through the handy checklist at the bottom. If anything significant is missing, the pull request may be closed until it's ready. The full guidebook on how pull requests are reviewed is here: [Code Review Guidelines](https://github.com/stan-dev/math/wiki/Developer-Doc#code-review-guidelines).
+Start by filling in the Summary, Tests, and Side Effects sections of this pull request and then work through the handy checklist at the bottom. If anything significant is missing, the pull request may be closed until it's ready. The full guidebook on how pull requests are reviewed is here: [Code Review Guidelines](https://github.com/stan-dev/stan/wiki/Developer-process-overview#code-review-guidelines).
 
 ## Summary
 
@@ -40,7 +40,7 @@ Replace this text with a short note on what will change if this pull request is
     - header checks pass, (`make test-headers`)
     - dependencies checks pass, (`make test-math-dependencies`)
     - docs build, (`make doxygen`)
-    - code passes the built in [C++ standards](https://github.com/stan-dev/stan/wiki/Code-Quality) checks (`make cpplint`)
+    - code passes the built in [C++ standards](https://github.com/stan-dev/stan/wiki/Coding-Style-and-Idioms) checks (`make cpplint`)
 
 - [ ] the code is written in idiomatic C++ and changes are documented in the doxygen
 

.github/workflows/header_checks.yml

@@ -13,8 +13,14 @@ on:
       - 'README.md'
       - 'RELEASE-NOTES.txt'
 
+permissions:
+  contents: read
+
 jobs:
   windows:
+    permissions:
+      actions: write  # for n1hility/cancel-previous-runs to create & stop workflow runs
+      contents: read  # for actions/checkout to fetch code
     name: Windows
     runs-on: windows-latest
 
@@ -28,7 +34,7 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: '2.x'
+        python-version: '3.x'
 
     - name: Print g++/mingw32-make version and path
       run: |
@@ -40,13 +46,16 @@ jobs:
 
     - name: Build Math libs
       shell: powershell
-      run: mingw32-make -f make/standalone math-libs
+      run: mingw32-make -f make/standalone math-libs -j2
 
     - name: Run header tests
       shell: powershell
       run: make -j2 test-headers
 
   opencl:
+    permissions:
+      actions: write  # for n1hility/cancel-previous-runs to create & stop workflow runs
+      contents: read  # for actions/checkout to fetch code
     name: OpenCL
     runs-on: ubuntu-latest
 
@@ -64,6 +73,9 @@ jobs:
         echo "STAN_OPENCL=true" > make/local
         make -j2 test-headers
   no_range_checks:
+    permissions:
+      actions: write  # for n1hility/cancel-previous-runs to create & stop workflow runs
+      contents: read  # for actions/checkout to fetch code
     name: NoRange
     runs-on: ubuntu-latest
 

.github/workflows/main.yml

@@ -12,8 +12,14 @@ on:
       - 'LICENSE.md'
       - 'README.md'
       - 'RELEASE-NOTES.txt'
+permissions:
+  contents: read
+
 jobs:
   prim-rev:
+    permissions:
+      actions: write  # for n1hility/cancel-previous-runs to create & stop workflow runs
+      contents: read  # for actions/checkout to fetch code
     name: prim and rev tests
     runs-on: windows-latest
 
@@ -26,7 +32,7 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: '2.x'
+        python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: 4.1.3
@@ -46,7 +52,9 @@ jobs:
 
     - name: Build Math libs
       shell: powershell
-      run: mingw32-make -f make/standalone math-libs
+      run: |
+        Add-Content make\local "O=1`n"
+        mingw32-make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
@@ -73,7 +81,7 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: '2.x'
+        python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: 4.1.3
@@ -93,7 +101,9 @@ jobs:
 
     - name: Build Math libs
       shell: powershell
-      run: mingw32-make -f make/standalone math-libs
+      run: |
+        Add-Content make\local "O=1`n"
+        mingw32-make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
@@ -103,12 +113,12 @@ jobs:
     - name: Run fwd unit tests and all the mix tests except those in mix/fun
       shell: powershell
       run: |
-        python.exe runTests.py test/unit/math/fwd
-        python.exe runTests.py test/unit/math/mix/core
-        python.exe runTests.py test/unit/math/mix/functor
-        python.exe runTests.py test/unit/math/mix/meta
-        python.exe runTests.py test/unit/math/mix/prob
-        python.exe runTests.py test/unit/math/mix/*_test.cpp
+        python.exe runTests.py test/unit/math/fwd -j2
+        python.exe runTests.py test/unit/math/mix/core -j2
+        python.exe runTests.py test/unit/math/mix/functor -j2
+        python.exe runTests.py test/unit/math/mix/meta -j2
+        python.exe runTests.py test/unit/math/mix/prob -j2
+        python.exe runTests.py test/unit/math/mix/*_test.cpp -j2
 
     - name: Upload gtest_output xml
       uses: actions/upload-artifact@v3
@@ -124,7 +134,7 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: '2.x'
+        python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: 4.1.3
@@ -144,7 +154,9 @@ jobs:
 
     - name: Build Math libs
       shell: powershell
-      run: mingw32-make -f make/standalone math-libs
+      run: |
+        Add-Content make\local "O=1`n"
+        mingw32-make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
@@ -170,7 +182,7 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: '2.x'
+        python-version: '3.x'
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: 4.1.3
@@ -190,7 +202,9 @@ jobs:
 
     - name: Build Math libs
       shell: powershell
-      run: mingw32-make -f make/standalone math-libs
+      run: |
+        Add-Content make\local "O=1`n"
+        mingw32-make -f make/standalone math-libs -j2
     - name: Add TBB to PATH
       shell: powershell
       run: echo "D:/a/math/math/lib/tbb" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8