Merge pull request #21 from RuhiRG/relFixes

CI: Fix for musllinux
d-SEAMS · Aug 26, 2024 · 5f2c5e8 · 5f2c5e8
2 parents 007ca96 + 74fd024
commit 5f2c5e8
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diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml
@@ -25,11 +25,15 @@ jobs:
         shell: bash -l {0}
         run: |
           micromamba activate pyseamsdev
-          meson wrap install fmt
-          meson wrap install eigen
           meson setup bbdir
           meson compile -C bbdir
 
+      - name: Run an import test (dev)
+        shell: bash -l {0}
+        run: |
+          python -c 'import bbdir.cyoda'
+
+
       - name: Run standard tests
         shell: bash -l {0}
         run: |

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -45,21 +45,32 @@ jobs:
     runs-on: ${{ matrix.os }}
     env: # Boost needs 13.0
       MACOSX_DEPLOYMENT_TARGET: '13.0'
-      CIBW_BEFORE_ALL: "scripts/cibw_before_build.sh"
+      CIBW_BEFORE_ALL_LINUX: "scripts/cibw_before_build.sh"
+      CIBW_BEFORE_ALL_MACOS: "scripts/cibw_before_build.sh"
     strategy:
       # Ensure that a wheel builder finishes even if another fails
       fail-fast: false
       matrix:
         # macos-13 is an intel runner, macos-14 is apple silicon
-        # TODO(ruhila) : windows-2022
+        # TODO: windows-2022
         os: [ubuntu-24.04, macos-13, macos-14]
 
     steps:
       - uses: actions/checkout@v4
+      # From https://github.com/pypa/cibuildwheel/discussions/989
+      - name: Install boost
+        if: ${{ runner.os == 'Windows' }}
+        uses: MarkusJx/[email protected]
+        id: install-boost
+        with:
+          boost_version: 1.83.0
+          link: static
       - name: Echo build platform
         run: echo Building wheels for ${{ matrix.os }}
       - name: Build wheels
         uses: pypa/[email protected]
+        env:
+          CIBW_ENVIRONMENT_WINDOWS: BOOST_ROOT='${{ steps.install-boost.outputs.BOOST_ROOT }}'
       - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
@@ -79,9 +90,6 @@ jobs:
       - name: Build sdist
         shell: bash -l {0}
         run: |
-          pipx install meson
-          meson wrap install fmt
-          meson wrap install eigen
           pipx run build --sdist
 
       - uses: actions/upload-artifact@v3

diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -30,8 +30,6 @@ jobs:
         shell: bash -el {0}
         run: |
           # Will also install the package
-          meson wrap install fmt
-          meson wrap install eigen
           pipx run pdm sync -v
           pipx run pdm run sphinx-build -b html docs/source html
       - name: Setup Pages

diff --git a/conda-lock.yml b/conda-lock.yml
@@ -13,17 +13,17 @@
 version: 1
 metadata:
   content_hash:
-    linux-64: 2f17ba0eb0654bd7b7f35f02e94373a9cfefb964304dd1bb8069f301c5ef7c15
-    osx-arm64: b3c9729118a92a63689096dffa0a76aa39b72c64a732817d1f2ebffd42cd26af
-    osx-64: 071c88948ae7de5e4d974a795f4875d403292f5d34a31d3b8b03e4c9a9f5bbc8
-    win-64: d967abaf0d30455ff6633d53d5893fd6d6cd9278ad54ae04cbe6dec3d044da3a
+    linux-64: b9d60a8c6af1519b5c9ee402e4b91dfa998c38924665c694d7941669ebb9ede5
+    osx-arm64: d9624a11c1940ee2e9b48e50483b51b2d31e20d63ceee867c5ca8a3abf6a0df9
+    osx-64: 97da03f9f9bdade2d4ecb07f09dcf20340774e51760ba4f8227a9a100a7b72ce
+    win-64: cfb33d71d9238628126e05c7ea90f562e50fc66b16995c7e61e2b2b38e24334e
   channels:
   - url: conda-forge
     used_env_vars: []
   platforms:
   - linux-64
-  - osx-arm64
   - osx-64
+  - osx-arm64
   - win-64
   sources:
   - environment.yml
@@ -1940,57 +1940,6 @@ package:
     sha256: 3ff11acdd5cc2f80227682966916e878e45ced94f59c402efb94911a5774e84e
   category: main
   optional: false
-- name: eigen
-  version: 3.4.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    libstdcxx-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h00ab1b0_0.conda
-  hash:
-    md5: b1b879d6d093f55dd40d58b5eb2f0699
-    sha256: 53b15a98aadbe0704479bacaf7a5618fcb32d1577be320630674574241639b34
-  category: main
-  optional: false
-- name: eigen
-  version: 3.4.0
-  manager: conda
-  platform: osx-64
-  dependencies:
-    libcxx: '>=15.0.7'
-  url: https://conda.anaconda.org/conda-forge/osx-64/eigen-3.4.0-h1c7c39f_0.conda
-  hash:
-    md5: 5b2cfc277e3d42d84a2a648825761156
-    sha256: 187c0677e0cdcdc39aed716687a6290dd5b7f52b49eedaef2ed76be6cd0a5a3d
-  category: main
-  optional: false
-- name: eigen
-  version: 3.4.0
-  manager: conda
-  platform: osx-arm64
-  dependencies:
-    libcxx: '>=15.0.7'
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/eigen-3.4.0-h1995070_0.conda
-  hash:
-    md5: 3691ea3ff568ba38826389bafc717909
-    sha256: c20b3677b16d8907343fce68e7c437184fef7f5ed0a765c104b775f8a485c5c9
-  category: main
-  optional: false
-- name: eigen
-  version: 3.4.0
-  manager: conda
-  platform: win-64
-  dependencies:
-    ucrt: '>=10.0.20348.0'
-    vc: '>=14.2,<15'
-    vc14_runtime: '>=14.29.30139'
-  url: https://conda.anaconda.org/conda-forge/win-64/eigen-3.4.0-h91493d7_0.conda
-  hash:
-    md5: 305b3ca7023ac046b9a42a48661f6512
-    sha256: 633a6a8db1f9a010cb0619f3446fb61f62dea348b09615ffae9744ab1001c24c
-  category: main
-  optional: false
 - name: exceptiongroup
   version: 1.2.2
   manager: conda
@@ -2166,56 +2115,6 @@ package:
     sha256: 7d006dbff4b97a598b7909c8c00e6f6c770f720ba60e2745137aad2183cbb8a8
   category: main
   optional: false
-- name: fmt
-  version: 9.1.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    libstdcxx-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/fmt-9.1.0-h924138e_0.tar.bz2
-  hash:
-    md5: b57864c85261a0fbc7132d2cc17478c7
-    sha256: bd48506faffa86e07f7b40d54f2d7e13b0fc956eda9760236750f5ea20db7129
-  category: main
-  optional: false
-- name: fmt
-  version: 9.1.0
-  manager: conda
-  platform: osx-64
-  dependencies:
-    libcxx: '>=14.0.4'
-  url: https://conda.anaconda.org/conda-forge/osx-64/fmt-9.1.0-hb8565cd_0.tar.bz2
-  hash:
-    md5: 310d897883dbdd88555d6321a4c2e6e8
-    sha256: 4891b66c94df8a346010caefb5d92df5e367be87ef0dea35a15d988f39a82719
-  category: main
-  optional: false
-- name: fmt
-  version: 9.1.0
-  manager: conda
-  platform: osx-arm64
-  dependencies:
-    libcxx: '>=14.0.4'
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/fmt-9.1.0-hffc8910_0.tar.bz2
-  hash:
-    md5: 78c11e6b1e971d49e9610d856a845d2f
-    sha256: 9864e8ed7501ef8d0e6c3de64b9a45865d05c9e19e074fb15633cf0b8924c459
-  category: main
-  optional: false
-- name: fmt
-  version: 9.1.0
-  manager: conda
-  platform: win-64
-  dependencies:
-    vc: '>=14.2,<15'
-    vs2015_runtime: '>=14.29.30037'
-  url: https://conda.anaconda.org/conda-forge/win-64/fmt-9.1.0-h181d51b_0.tar.bz2
-  hash:
-    md5: 31a20cf261b2bd0a76d670db1b3e6fa1
-    sha256: b4882f05294a46949cf4d15e4b2c50f29257b0d042d7d8184e4722b392d71193
-  category: main
-  optional: false
 - name: fortran-compiler
   version: 1.7.0
   manager: conda
@@ -4945,33 +4844,36 @@ package:
   manager: conda
   platform: linux-64
   dependencies:
+    __glibc: '>=2.17,<3.0.a0'
     libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda
+  url: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda
   hash:
-    md5: fcea371545eda051b6deafb24889fc69
-    sha256: 4fc3b384f4072b68853a0013ea83bdfd3d66b0126e2238e1d6e1560747aa7586
+    md5: 70caf8bb6cf39a0b6b7efc885f51c0fe
+    sha256: 6a1d5d8634c1a07913f1c525db6455918cbc589d745fac46d9d6e30340c8731a
   category: main
   optional: false
 - name: ncurses
   version: '6.5'
   manager: conda
   platform: osx-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/osx-64/ncurses-6.5-h5846eda_0.conda
+  dependencies:
+    __osx: '>=10.13'
+  url: https://conda.anaconda.org/conda-forge/osx-64/ncurses-6.5-hf036a51_1.conda
   hash:
-    md5: 02a888433d165c99bf09784a7b14d900
-    sha256: 6ecc73db0e49143092c0934355ac41583a5d5a48c6914c5f6ca48e562d3a4b79
+    md5: e102bbf8a6ceeaf429deab8032fc8977
+    sha256: b0b3180039ef19502525a2abd5833c00f9624af830fd391f851934d57bffb9af
   category: main
   optional: false
 - name: ncurses
   version: '6.5'
   manager: conda
   platform: osx-arm64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-hb89a1cb_0.conda
+  dependencies:
+    __osx: '>=11.0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h7bae524_1.conda
   hash:
-    md5: b13ad5724ac9ae98b6b4fd87e4500ba4
-    sha256: 87d7cf716d9d930dab682cb57b3b8d3a61940b47d6703f3529a155c938a6990a
+    md5: cb2b0ea909b97b3d70cd3921d1445e1a
+    sha256: 27d0b9ff78ad46e1f3a6c96c479ab44beda5f96def88e2fe626e0a49429d8afc
   category: main
   optional: false
 - name: ninja
@@ -7728,57 +7630,6 @@ package:
     sha256: 4e2246383003acbad9682c7c63178e2e715ad0eb84f03a8df1fbfba455dfedc5
   category: main
   optional: false
-- name: yaml-cpp
-  version: 0.8.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    libstdcxx-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h59595ed_0.conda
-  hash:
-    md5: 965eaacd7c18eb8361fd12bb9e7a57d7
-    sha256: a65bb5284369e548a15a44b14baf1f7ac34fa4718d7d987dd29032caba2ecf20
-  category: main
-  optional: false
-- name: yaml-cpp
-  version: 0.8.0
-  manager: conda
-  platform: osx-64
-  dependencies:
-    libcxx: '>=15.0.7'
-  url: https://conda.anaconda.org/conda-forge/osx-64/yaml-cpp-0.8.0-he965462_0.conda
-  hash:
-    md5: 1bb3addc859ed1338370da6e2996ef47
-    sha256: 6e5e4afa1011a1ad5a734e895b8d2b2ad0fbc9ef6538aac8f852b33b2ebe44a8
-  category: main
-  optional: false
-- name: yaml-cpp
-  version: 0.8.0
-  manager: conda
-  platform: osx-arm64
-  dependencies:
-    libcxx: '>=15.0.7'
-  url: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-cpp-0.8.0-h13dd4ca_0.conda
-  hash:
-    md5: e783a232972a5c7dca549111e63a78b2
-    sha256: e65a52fb1c9821ba3a7a670d650314f8ff983865e77ba9f69f74e0906844943d
-  category: main
-  optional: false
-- name: yaml-cpp
-  version: 0.8.0
-  manager: conda
-  platform: win-64
-  dependencies:
-    ucrt: '>=10.0.20348.0'
-    vc: '>=14.2,<15'
-    vc14_runtime: '>=14.29.30139'
-  url: https://conda.anaconda.org/conda-forge/win-64/yaml-cpp-0.8.0-h63175ca_0.conda
-  hash:
-    md5: 9032e2129ea7afcc1a8e3d85715a931d
-    sha256: d2e506baddde40388700f2c83586a002b927810d453272065b9e7b69d422fcca
-  category: main
-  optional: false
 - name: zipp
   version: 3.20.0
   manager: conda

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -7,7 +7,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "PydSEAMSlib"
-release = "0.1.0"
+release = "0.0.2"
 copyright = "2024, d-SEAMS developers"
 author = "Ruhila"
 

diff --git a/environment.yml b/environment.yml
@@ -13,10 +13,7 @@ dependencies:
   - pkg-config
   - clang
   # d-SEAMS deps
-  - yaml-cpp
   - boost-cpp
-  - fmt==9.1.0
-  - eigen==3.4.0
   # Python
   - pdm
   - pybind11

diff --git a/meson.build b/meson.build
@@ -1,7 +1,7 @@
 project(
     'PydSEAMSlib',
     'cpp',
-    version: '1.0.1',
+    version: '0.0.2',
     default_options: ['warning_level=1', 'cpp_std=c++14'],
 )
 

diff --git a/pyb11_srcs/py_one.cc b/pyb11_srcs/py_one.cc
@@ -26,6 +26,8 @@
 #include "../subprojects/seams-core/src/include/internal/topo_one_dim.hpp"
 #include "../subprojects/seams-core/src/include/internal/topo_two_dim.hpp"
 
+#include <cstdint>
+
 #include <fmt/core.h>
 
 namespace py = pybind11;
@@ -128,7 +130,7 @@ PYBIND11_MODULE(cyoda, m) {
         .def("__repr__",
              [](const molSys::Point<double> &self_C) {
                  std::uintptr_t ptr_val = std::uintptr_t(&self_C);
-                 return fmt::format("<PointDouble mem_loc:{:x}>", static_cast<uint>(ptr_val));
+                 return fmt::format("<PointDouble mem_loc:{:x}>", static_cast<uint64_t>(ptr_val));
              })
         .def("__str__", [](const molSys::Point<double> &self_C) {
             return fmt::format("x: {} y: {} z: {} type: {} molID: {} atomID: {} inSlice: {}",
@@ -163,7 +165,7 @@ PYBIND11_MODULE(cyoda, m) {
         .def_readwrite("c_value", &molSys::Result::c_value)
         .def("__repr__", [](const molSys::Result &self_C) {
             std::uintptr_t ptr_val = std::uintptr_t(&self_C);
-            return fmt::format("<Result mem_loc:{:x}>", static_cast<uint>(ptr_val));
+            return fmt::format("<Result mem_loc:{:x}>", static_cast<uint64_t>(ptr_val));
         });
     //        .def("__str__", [](const molSys::Result &self_C) {
     //            return fmt::format("classifier: {} c_value: {}", self_C.classifier,

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "pydseamslib"
-version = "0.0.1"
+version = "0.0.2"
 description = "Python bindings for seams-core"
 authors = [
     {name = "Amrita Goswami", email = "[email protected]"},

diff --git a/scripts/cibw_before_build.sh b/scripts/cibw_before_build.sh
@@ -3,12 +3,10 @@
 if [[ "$OSTYPE" == "darwin"* ]]; then
     # macOS
     brew install boost
+elif ldd --version 2>&1 | grep -q musl; then
+    # musllinux
+    apk add --no-cache boost-dev
 else
-    # Linux (assuming yum-based system)
+    # manylinux
     yum -y install boost-devel
 fi
-
-# Common commands for both systems
-pip install meson
-meson wrap install eigen
-meson wrap install fmt