tweag · ConnorBaker · Feb 5, 2024 · Feb 5, 2024 · Feb 5, 2024 · Feb 6, 2024
diff --git a/.github/workflows/workflow.yaml b/.github/workflows/workflow.yaml
@@ -6,80 +6,155 @@ on:
   pull_request:
 
 jobs:
-  build:
-    name: Build - Windows
-    runs-on: windows-latest
-    steps:
-      - name: Install dependencies
-        run: |
-          choco install -y haskell-stack
-          choco install -y r --version 4.0.0
-      - uses: actions/checkout@v4
-      - name: Get Stack snapshot install directory
-        id: stack-snapshot
-        # NOTE: `stack path` must run at least once prior to caching to ensure the directory
-        # exists and is populated.
-        run: |
-          stack path --snapshot-install-root
-          "dir=$(stack path --snapshot-install-root)" | Out-File -FilePath $env:GITHUB_OUTPUT -Append
-      - uses: actions/cache@v4
-        with:
-          path: ${{ steps.stack-snapshot.outputs.dir }}
-          key: ${{ runner.os }}-stack-${{ hashFiles('**/*.cabal') }}
-          restore-keys: ${{ runner.os }}-stack-
-      - name: Build
-        run: |
-          stack build inline-r H `
-            --extra-lib-dirs="C:/Program files/R/R-4.0.0/bin/x64" `
-            --extra-include-dirs="C:/Program files/R/R-4.0.0/include"
-  test:
-    name: Build & Test - ${{ matrix.os }} - ${{ matrix.stack_yaml }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os:
-          - macos-latest
-          - ubuntu-latest
-        stack_yaml:
-          - stack.yaml
-          - stack-lts-19.yaml
-          - stack-lts-20.yaml
-          - stack-lts-21.yaml
-          - stack-nightly.yaml
-    runs-on: ${{ matrix.os }}
+  # stack-windows:
+  #   name: Stack - Windows - stack.yaml
+  #   runs-on: windows-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - name: Install Stack
+  #       run: choco install -y haskell-stack
+  #     - name: Install R
+  #       run: choco install -y r --version 4.0.0
+  #     # NOTE: `stack path` must run at least once prior to caching to ensure the directory
+  #     # exists and is populated.
+  #     - name: Prime Stack snapshot cache
+  #       run: stack path --snapshot-install-root
+  #     - name: Get Stack snapshot install directory
+  #       id: stack-snapshot
+  #       run: Add-Content -Path $env:GITHUB_OUTPUT -Value ("dir=$(stack path --snapshot-install-root)")
+  #     - uses: actions/cache@v4
+  #       with:
+  #         path: ${{ steps.stack-snapshot.outputs.dir }}
+  #         key: ${{ runner.os }}-stack-${{ hashFiles('**/*.cabal') }}
+  #         restore-keys: ${{ runner.os }}-stack-
+  #     - name: Build
+  #       run: |
+  #         stack build inline-r H `
+  #           --extra-lib-dirs="C:/Program files/R/R-4.0.0/bin/x64" `
+  #           --extra-include-dirs="C:/Program files/R/R-4.0.0/include"
+
+  # stack-macOS:
+  #   name: Stack - macOS - ${{ matrix.stack_yaml }}
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       stack_yaml:
+  #         - stack.yaml
+  #         - stack-lts-19.yaml
+  #         - stack-lts-20.yaml
+  #         - stack-lts-21.yaml
+  #         - stack-nightly.yaml
+  #   runs-on: macos-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: DeterminateSystems/nix-installer-action@main
+  #     - uses: DeterminateSystems/magic-nix-cache-action@main
+  #     - name: Install Stack
+  #       run: nix-env --file ./nixpkgs.nix --install --attr stack
+  #     # NOTE: The renaming of the stack.yaml file is a workaround for
+  #     # https://github.com/commercialhaskell/stack/issues/5028.
+  #     - name: Make desired stack.yaml available
+  #       if: ${{ matrix.stack_yaml != 'stack.yaml' }}
+  #       run: mv ${{ matrix.stack_yaml }} stack.yaml
+  #     # NOTE: `stack path` must run at least once prior to caching to ensure the directory
+  #     # exists and is populated.
+  #     - name: Prime Stack snapshot cache
+  #       run: stack --nix path --snapshot-install-root
+  #     - name: Get Stack snapshot install directory
+  #       id: stack-snapshot
+  #       run: echo "dir=$(stack --nix path --snapshot-install-root)" > "${GITHUB_OUTPUT}"
+  #     - uses: actions/cache@v4
+  #       with:
+  #         path: ${{ steps.stack-snapshot.outputs.dir }}
+  #         key: ${{ runner.os }}-stack-${{ hashFiles('**/*.cabal') }}
+  #         restore-keys: ${{ runner.os }}-stack-
+  #     - name: Stack build
+  #       run: stack --nix build
+
+  # stack-linux:
+  #   name: Stack - Linux - ${{ matrix.stack_yaml }}
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       stack_yaml:
+  #         - stack.yaml
+  #         - stack-lts-19.yaml
+  #         - stack-lts-20.yaml
+  #         - stack-lts-21.yaml
+  #         - stack-nightly.yaml
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: DeterminateSystems/nix-installer-action@main
+  #     - uses: DeterminateSystems/magic-nix-cache-action@main
+  #     - name: Install Stack
+  #       run: nix-env --file ./nixpkgs.nix --install --attr stack
+  #     # NOTE: The renaming of the stack.yaml file is a workaround for
+  #     # https://github.com/commercialhaskell/stack/issues/5028.
+  #     - name: Make desired stack.yaml available
+  #       if: ${{ matrix.stack_yaml != 'stack.yaml' }}
+  #       run: mv ${{ matrix.stack_yaml }} stack.yaml
+  #     # NOTE: `stack path` must run at least once prior to caching to ensure the directory
+  #     # exists and is populated.
+  #     - name: Prime Stack snapshot cache
+  #       run: stack --nix path --snapshot-install-root
+  #     - name: Get Stack snapshot install directory
+  #       id: stack-snapshot
+  #       run: echo "dir=$(stack --nix path --snapshot-install-root)" > "${GITHUB_OUTPUT}"
+  #     - uses: actions/cache@v4
+  #       with:
+  #         path: ${{ steps.stack-snapshot.outputs.dir }}
+  #         key: ${{ runner.os }}-stack-${{ hashFiles('**/*.cabal') }}
+  #         restore-keys: ${{ runner.os }}-stack-
+  #     - name: Stack build
+  #       run: stack --nix build
+  #     - name: Stack test
+  #       run: stack --nix test
+  #     - name: Add ~/.local/bin to PATH
+  #       run: echo "$HOME/.local/bin" >> "${GITHUB_PATH}"
+  #     - name: Stack install
+  #       run: stack --nix install
+  #     - name: IHaskell install
+  #       run: stack --nix exec -- ihaskell install
+  #     - name: Test IHaskell jupyter notebook example
+  #       run: stack --nix exec -- jupyter nbconvert --to notebook --execute --inplace ./ihaskell-inline-r/examples/tutorial-ihaskell-inline-r.ipynb
+
+  cabal-linux:
+    name: Cabal - Linux
+    runs-on: ubuntu-latest
+    env:
+      NIX_SHELL_RUN: nix-shell ./shell-cabal.nix -I nixpkgs=./nixpkgs.nix --run
     steps:
       - uses: actions/checkout@v4
       - uses: DeterminateSystems/nix-installer-action@main
       - uses: DeterminateSystems/magic-nix-cache-action@main
-      - name: Install Stack
-        run: |
-          nix-env --file ./nixpkgs.nix --install --attr stack
-      - name: Get Stack snapshot install directory
-        id: stack-snapshot
-        # NOTE: `stack path` must run at least once prior to caching to ensure the directory
-        # exists and is populated.
-        # NOTE: The renaming of the stack.yaml file is a workaround for
-        # https://github.com/commercialhaskell/stack/issues/5028.
-        run: |
-          [ ${{ matrix.stack_yaml }} = stack.yaml ] || mv ${{ matrix.stack_yaml }} stack.yaml
-          stack --nix path --snapshot-install-root
-          echo "dir=$(stack --nix path --snapshot-install-root)" > "${GITHUB_OUTPUT}"
-      - uses: actions/cache@v4
+      - name: Update cabal
+        run: ${{ env.NIX_SHELL_RUN }} "cabal update"
+      - name: Configure the build
+        run: ${{ env.NIX_SHELL_RUN }} "cabal configure --enable-tests --disable-documentation"
+      - name: Generate dist-newstyle/cache/plan.json
+        run: ${{ env.NIX_SHELL_RUN }} "cabal build all --dry-run"
+      - name: Restore cached dependencies
+        uses: actions/cache/restore@v4
+        id: cache
+        env:
+          key: ${{ runner.os }}-cabal-${{ hashFiles('**/*.cabal') }}
+        with:
+          path: ${{ env.HOME }}/.cabal/store
+          key: ${{ env.key }}-plan-${{ hashFiles('**/plan.json') }}
+          restore-keys: ${{ env.key }}-
+      - name: Install Haskell dependencies
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: ${{ env.NIX_SHELL_RUN }} "cabal build all --only-dependencies"
+      # Cache dependencies already here, so that we do not have to rebuild them should the subsequent steps fail.
+      - name: Cache Haskell dependencies
+        uses: actions/cache/save@v4
+        # If we had an exact cache hit, trying to save the cache would error because of key clash.
+        if: steps.cache.outputs.cache-hit != 'true'
         with:
-          path: ${{ steps.stack-snapshot.outputs.dir }}
-          key: ${{ runner.os }}-stack-${{ hashFiles('**/*.cabal') }}
-          restore-keys: ${{ runner.os }}-stack-
-      - name: Build
-        run: |
-          stack --nix build
-      - name: Test
-        if: ${{ runner.os == 'Linux' }}
-        run: |
-          stack --nix test
-      - name: Test IHaskell jupyter notebook example
-        if: ${{ runner.os == 'Linux' }}
-        run: |
-          stack --nix install
-          export PATH="$HOME/.local/bin:$PATH"
-          stack --nix exec -- ihaskell install
-          stack --nix exec -- jupyter nbconvert --to notebook --execute --inplace ./IHaskell/examples/tutorial-ihaskell-inline-r.ipynb
+          path: ${{ env.HOME }}/.cabal/store
+          key: ${{ steps.cache.outputs.cache-primary-key }}
+      - name: Cabal build
+        run: ${{ env.NIX_SHELL_RUN }} "cabal build all"
+      - name: Cabal test
+        run: ${{ env.NIX_SHELL_RUN }} "cabal test all"
diff --git a/examples/HaskellR-examples.cabal → HaskellR-examples/HaskellR-examples.cabal b/examples/HaskellR-examples.cabal → HaskellR-examples/HaskellR-examples.cabal
@@ -16,7 +16,7 @@ extra-source-files:
 source-repository head
   type:     git
   location: git://github.com/tweag/HaskellR.git
-  subdir: examples
+  subdir: HaskellR-examples
 
 common common-config
   default-language:    Haskell2010

diff --git a/examples/LICENSE → HaskellR-examples/LICENSE b/examples/LICENSE → HaskellR-examples/LICENSE
diff --git a/examples/RelaxWithNM.hs → HaskellR-examples/RelaxWithNM.hs b/examples/RelaxWithNM.hs → HaskellR-examples/RelaxWithNM.hs
diff --git a/examples/fft/Main.hs → HaskellR-examples/fft/Main.hs b/examples/fft/Main.hs → HaskellR-examples/fft/Main.hs
diff --git a/examples/fib/Fib.hs → HaskellR-examples/fib/Fib.hs b/examples/fib/Fib.hs → HaskellR-examples/fib/Fib.hs
diff --git a/examples/fib/Main.hs → HaskellR-examples/fib/Main.hs b/examples/fib/Main.hs → HaskellR-examples/fib/Main.hs
diff --git a/examples/nls/Main.hs → HaskellR-examples/nls/Main.hs b/examples/nls/Main.hs → HaskellR-examples/nls/Main.hs
diff --git a/examples/nls/nls.H → HaskellR-examples/nls/nls.H b/examples/nls/nls.H → HaskellR-examples/nls/nls.H
diff --git a/examples/nls/system.hs → HaskellR-examples/nls/system.hs b/examples/nls/system.hs → HaskellR-examples/nls/system.hs
diff --git a/examples/nls2/Main.hs → HaskellR-examples/nls2/Main.hs b/examples/nls2/Main.hs → HaskellR-examples/nls2/Main.hs
diff --git a/examples/nls2/nls2.H → HaskellR-examples/nls2/nls2.H b/examples/nls2/nls2.H → HaskellR-examples/nls2/nls2.H
diff --git a/examples/nls2/system.hs → HaskellR-examples/nls2/system.hs b/examples/nls2/system.hs → HaskellR-examples/nls2/system.hs
diff --git a/cabal.project b/cabal.project
@@ -0,0 +1,11 @@
+packages:
+  H/H.cabal
+  HaskellR-examples/HaskellR-examples.cabal
+  ihaskell-inline-r/ihaskell-inline-r.cabal
+  inline-r/inline-r.cabal
+
+index-state:
+  , hackage.haskell.org 2024-02-06T04:11:57Z
+
+constraints:
+  ihaskell-blaze == 0.3.0.1
diff --git a/docs/docs/build-and-install.md b/docs/docs/build-and-install.md
@@ -114,10 +114,10 @@ $ stack [--docker|--nix] exec jupyter notebook
 After launching the Jupyter notebook server you can visit
 
 ~~~
-http://localhost:8888/notebooks/IHaskell/examples/tutorial-ihaskell-inline-r.ipynb
+http://localhost:8888/notebooks/ihaskell-inline-r/examples/tutorial-ihaskell-inline-r.ipynb
 ~~~
 
 in your browser for an interactive tutorial, which is available in
 static form [here][tutorial].
 
-[tutorial]: https://github.com/tweag/HaskellR/blob/master/IHaskell/examples/tutorial-ihaskell-inline-r.ipynb
+[tutorial]: https://github.com/tweag/HaskellR/blob/master/ihaskell-inline-r/examples/tutorial-ihaskell-inline-r.ipynb
diff --git a/docs/docs/inline-r-with-IHaskell.md b/docs/docs/inline-r-with-IHaskell.md
@@ -8,7 +8,7 @@ the [IHaskell][ihaskell] kernel for interactively authoring notebooks
 replete with plots, formulas, R code and Haskell code.
 
 See "Building and installing" to get started and the
-[tutorial notebook](https://github.com/tweag/HaskellR/blob/master/IHaskell/examples/tutorial-ihaskell-inline-r.ipynb)
+[tutorial notebook](https://github.com/tweag/HaskellR/blob/master/ihaskell-inline-r/examples/tutorial-ihaskell-inline-r.ipynb)
 in the repository for a walkthrough.
 
 [ihaskell]: https://github.com/gibiansky/IHaskell
diff --git a/docs/docs/using-h.md b/docs/docs/using-h.md
@@ -124,10 +124,10 @@ Running examples
 
 Some interactive examples of using H are located in the folders:
 
-* `examples/nls`
-* `examples/nls2`
+* `HaskellR-examples/nls`
+* `HaskellR-examples/nls2`
 
 The following commands can be used to run these examples:
 
-    $ cd examples/<example-name>
+    $ cd HaskellR-examples/<example-name>
     $ H -- -ghci-script <example-name>.H
diff --git a/IHaskell/.gitignore → ihaskell-inline-r/.gitignore b/IHaskell/.gitignore → ihaskell-inline-r/.gitignore
diff --git a/IHaskell/ChangeLog.markdown → ihaskell-inline-r/ChangeLog.markdown b/IHaskell/ChangeLog.markdown → ihaskell-inline-r/ChangeLog.markdown
diff --git a/IHaskell/LICENSE → ihaskell-inline-r/LICENSE b/IHaskell/LICENSE → ihaskell-inline-r/LICENSE
diff --git a/IHaskell/Setup.hs → ihaskell-inline-r/Setup.hs b/IHaskell/Setup.hs → ihaskell-inline-r/Setup.hs
diff --git a/...examples/tutorial-ihaskell-inline-r.ipynb → ...examples/tutorial-ihaskell-inline-r.ipynb b/...examples/tutorial-ihaskell-inline-r.ipynb → ...examples/tutorial-ihaskell-inline-r.ipynb
diff --git a/IHaskell/ihaskell-inline-r.cabal → ihaskell-inline-r/ihaskell-inline-r.cabal b/IHaskell/ihaskell-inline-r.cabal → ihaskell-inline-r/ihaskell-inline-r.cabal
@@ -33,4 +33,4 @@ library
 source-repository head
   type: git
   location: https://github.com/tweag/HaskellR.git
-  subdir: IHaskell
+  subdir: ihaskell-inline-r
diff --git a/IHaskell/src/IHaskell/Display/InlineR.hs → ...-inline-r/src/IHaskell/Display/InlineR.hs b/IHaskell/src/IHaskell/Display/InlineR.hs → ...-inline-r/src/IHaskell/Display/InlineR.hs
diff --git a/nix/R.nix b/nix/R.nix
@@ -0,0 +1,93 @@
+{
+  pkgs ? import ./nixpkgs.nix { },
+  RVersion ? "4.2.3",
+}:
+let
+  inherit (pkgs) fetchpatch fetchurl;
+  inherit (pkgs.lib) lists strings versions;
+in
+# Set enableStrictBarrier to true to build HaskellR against a version of R with
+# the --enable-strict-barrier configure flag enabled for better memory
+# diagnostics.
+(pkgs.R.override { enableStrictBarrier = false; }).overrideAttrs (
+  # Pin R to a specific version to avoid breaking changes in the R API.
+  finalAttrs: prevAttrs: {
+    version = RVersion;
+    src = fetchurl {
+      url = "https://cran.r-project.org/src/base/R-${versions.major finalAttrs.version}/R-${finalAttrs.version}.tar.gz";
+      hash = builtins.getAttr RVersion {
+        "4.0.0" = "sha256-Br6wKRtWmXhITrDctdIzlmXsdFc3vftOhz56WnVJKUA=";
+        "4.0.1" = "sha256-lf4kpNjY+PiIRgyPX+QxHOxlbnoXItIzIYvAOGG8bzI=";
+        "4.0.2" = "sha256-07zqs2TaCHZiXkCXgItCUSOV/fQSkvSRWrH9JXwbvnU=";
+        "4.0.3" = "sha256-CZg6injV+2vEXSexxV+bpSZfePpUpVwTrmkfh8W7ng0=";
+        "4.0.4" = "sha256-Uj8n1pdEoIyPC9Xh5sPYmk2yntmDOIunCWOjzTpKgC4=";
+        "4.0.5" = "sha256-Cj7geap3LhMf5UNTEatif8vMtaUMq8VCkub2IEbx/+8=";
+        "4.1.0" = "sha256-6OaJWdcoLKFHNg/JZEram9FhureBurFNM7iZmpUYJ4E=";
+        "4.1.1" = "sha256-UV4DJldSJX0LcDbzgPguQrRu2Ec/VPJce2ftJbu902Q=";
+        "4.1.2" = "sha256-IDYiXp9yB9TOCX5Ulyrs2qi0DX2ZEc0mSR+sWg+rOK8=";
+        "4.1.3" = "sha256-Ff9bMzxhCUBgsqUunB2OxVzELdAp45yiKr2qkJUm/tY=";
+        "4.2.0" = "sha256-OOq3cZt60JU4jwaqCQxaKyAnkZRd5g0+K7DqsfUJdIg=";
+        "4.2.1" = "sha256-TVLbSG0nhI5UYT1O6XetlS7AjOF4B+G1JbEM1ENsZD8=";
+        "4.2.2" = "sha256-D/YrQuxRr6VxPK7nxP3noMRZQLo5vvjFyUh/7wyVPfU=";
+        "4.2.3" = "sha256-VeSpptQ74xTiwD0CZqb6VESv3OULMDv8O4Kzl5UW4HQ=";
+        "4.3.0" = "sha256-RdzEi2zyfTYQIPd/3ho5IJ6Ze4FAKzZjyhwBAFampgk=";
+        "4.3.1" = "sha256-jdC/JPECPG9hjDsxc4PSkbSklPQNc7mDrCL/6pnkupk=";
+        "4.3.2" = "sha256-s/V2CsLu6AJqPw7vyyW0dyPZeAOO7o6ER2IJTIYMRSo=";
+      };
+    };
+
+    patches =
+      prevAttrs.patches or [ ]
+      # R: 4.0.4 -> 4.1.0
+      # See https://github.com/NixOS/nixpkgs/commit/9a88197fe7825f486052e3a9eca4a68192335978
+      ++
+        lists.optionals
+          (
+            RVersion == "4.1.0"
+            && strings.hasInfix "--without-recommended-packages" (prevAttrs.preConfigure or "")
+          )
+          [
+            (fetchpatch {
+              name = "fix-tests-without-recommended-packages.patch";
+              url = "https://github.com/wch/r-source/commit/7715c67cabe13bb15350cba1a78591bbb76c7bac.patch";
+              # this part of the patch reverts something that was committed after R 4.1.0, so ignore it.
+              excludes = [ "tests/Pkgs/xDir/pkg/DESCRIPTION" ];
+              hash = "sha256-iguLndCIuKuCxVCi/4NSu+9RzBx5JyeHx3K6IhpYshQ=";
+            })
+            (fetchpatch {
+              name = "use-codetools-conditionally.patch";
+              url = "https://github.com/wch/r-source/commit/7543c28b931db386bb254e58995973493f88e30d.patch";
+              hash = "sha256-+yHXB5AItFyQjSxfogxk72DrSDGiBh7OiLYFxou6Xlk=";
+            })
+          ]
+      # R: 4.1.3 -> 4.2.0
+      # See: https://github.com/NixOS/nixpkgs/commit/5eb9f35c44d30153ff1df2105ed73e148a79a3ee
+      ++ lists.optionals (RVersion == "4.2.0" || RVersion == "4.2.1") [
+        (fetchpatch {
+          name = "test-reg-packages.patch";
+          url = "https://raw.githubusercontent.com/NixOS/nixpkgs/5eb9f35c44d30153ff1df2105ed73e148a79a3ee/pkgs/applications/science/math/R/test-reg-packages.patch";
+          hash = "sha256-FUzrenAFvD8GL1/RMG8DRRx+ITcEkDkRGKTVyAhyKqA=";
+        })
+      ];
+
+    postPatch =
+      prevAttrs.postPatch or ""
+      # Nixpkgs ships with curl >= 8.x, which is not compatible with R pre-4.3. However, in the release notes for R
+      # 4.3 (https://stat.ethz.ch/pipermail/r-announce/2023/000691.html), it is mentioned that despite the major
+      # version change for curl, the API is still compatible with the previous version. Therefore, we can patch the
+      # check for curl 7.x. This fixes the following error:
+      #   error: libcurl >= 7.28.0 library and headers are required with support for https
+      # We must patch the ./configure script and the ./m4/R.m4 file to make this work.
+      + strings.optionalString (strings.versionOlder RVersion "4.3.0") ''
+        substituteInPlace \
+          ./configure \
+          ./m4/R.m4 \
+          --replace-fail \
+            "#if LIBCURL_VERSION_MAJOR > 7" \
+            "#if LIBCURL_VERSION_MAJOR < 7" \
+          --replace-fail \
+            "#elif LIBCURL_VERSION_MAJOR == 7 && LIBCURL_VERSION_MINOR >= 28" \
+            "#elif LIBCURL_VERSION_MAJOR == 7 && LIBCURL_VERSION_MINOR >= 28 || LIBCURL_VERSION_MAJOR == 8"
+      '';
+  }
+)