Use conda-lock for reproducible conda env

.devcontainer/devcontainer.json

@@ -8,7 +8,7 @@
 	"remoteUser": "vscode",
 
 	// Setup conda environment
-	"onCreateCommand": ".devcontainer/onCreate-conda.sh",
+	"onCreateCommand": ".devcontainer/onCreate-conda.sh || true",
 
 	// Install additional features.
 	"features": {

.devcontainer/onCreate-conda.sh

@@ -2,9 +2,8 @@
 set -e
 
 # Create conda environment
-./bootstrap-conda
 conda install mamba -n base -c conda-forge -y
-mamba env create --file src/environment-dev-3.11.yml || mamba env update --file src/environment-dev-3.11.yml
+mamba env create --file src/environment-dev-3.11-linux.yml || mamba env update --file src/environment-dev-3.11-linux.yml
 conda init bash
 
 # Build sage

.github/workflows/ci-conda.yml

@@ -18,11 +18,11 @@ concurrency:
 jobs:
   test:
     name: Conda
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}-latest
 
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu, macos]
         python: ['3.9', '3.10', '3.11']
         # Optional environment is disabled for now as its not yet working
         # environment: [environment, environment-optional]
@@ -38,9 +38,6 @@ jobs:
           GH_TOKEN: ${{ github.token }}
           SAGE_CI_FIXES_FROM_REPOSITORIES: ${{ vars.SAGE_CI_FIXES_FROM_REPOSITORIES }}
 
-      - name: Create conda environment files
-        run: ./bootstrap-conda
-
       - name: Cache conda packages
         uses: actions/cache@v3
         with:
@@ -57,7 +54,7 @@ jobs:
           channels: conda-forge
           channel-priority: true
           activate-environment: sage
-          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}.yml
+          environment-file: src/${{ matrix.conda-env }}-${{ matrix.python }}-${{ startsWith(matrix.os, 'macos') && 'macos' || 'linux' }}.yml
 
       - name: Print Conda environment
         shell: bash -l {0}

.github/workflows/conda-lock-update.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+
+from pathlib import Path
+import subprocess
+
+script_dir = Path(__file__).resolve().parent
+root_dir = script_dir / '..' / '..'
+
+subprocess.run([str(root_dir / "bootstrap-conda")])
+
+platforms = {
+    "linux-64": "linux",
+    "linux-aarch64": "linux-aarch64",
+    "osx-64": "macos",
+    "osx-arm64": "macos-arm64"
+    #"win-64": "win",
+}
+pythons = ["3.9", "3.10", "3.11"]
+tags = ["", "-dev"]
+sources = ["", "src"]
+
+for platform_key, platform_value in platforms.items():
+    for python in pythons:
+        for tag in tags:
+            for src in sources:
+                env_file = root_dir / src / f"environment{tag}-{python}.yml"
+                lock_file = root_dir / src / f"environment{tag}-{python}-{platform_value}"
+
+                if not env_file.exists():
+                    continue
+
+                print(f"Updating lock file for {env_file} at {lock_file}", flush=True)
+                subprocess.run(["conda-lock", "--channel", "conda-forge", "--kind", "env", "--platform", platform_key, "--file", str(env_file), "--lockfile", str(lock_file), "--filename-template", str(lock_file)])

.gitpod.yml

@@ -7,8 +7,7 @@ tasks:
   - name: Setup
     # Create conda environment, then configure and build sage
     init: >-
-      ./bootstrap-conda
-      && mamba env create --file src/environment-dev-3.11.yml --prefix venv
+      && mamba env create --file src/environment-dev-3.11-linux.yml --prefix venv
       && conda config --append envs_dirs $(pwd)
       && conda activate $(pwd)/venv
       && ./bootstrap

.vscode/settings.json

@@ -35,5 +35,6 @@
         "sagemath",
         "Cython"
     ],
-    "editor.formatOnType": true
+    "editor.formatOnType": true,
+    "esbonio.sphinx.confDir": ""
 }

bootstrap-conda

@@ -115,6 +115,7 @@ echo >&2 $0:$LINENO: generate conda environment files
     (
         sed 's/name: sage/name: sage-dev/' src/environment-template.yml
         echo "  # Additional dev tools"
+        echo "  - conda-lock"
         for pkg in $DEVELOP_SYSTEM_PACKAGES; do
             echo "  - $pkg"
         done

build/pkgs/sphinx/distros/conda.txt

@@ -1 +1 @@
-sphinx<8,>=5.2
+sphinx>=5.2

environment-3.10-linux-aarch.yml

@@ -0,0 +1,193 @@
+# Generated by conda-lock.
+# platform: linux-aarch64
+# input_hash: d745aab1c14fd9333fe506502bdbc2bb5ab40c689cf58e8b1eb71d8e283a8e6d
+
+channels:
+  - conda-forge
+dependencies:
+  - _sysroot_linux-aarch64_curr_repodata_hack=4=h57d6b7b_13
+  - ca-certificates=2023.7.22=hcefe29a_0
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=hab24e00_0
+  - kernel-headers_linux-aarch64=4.18.0=h5b4a56d_13
+  - ld_impl_linux-aarch64=2.40=h2d8c526_0
+  - libboost-headers=1.82.0=h8af1aa0_2
+  - libgcc-devel_linux-aarch64=12.3.0=h8b5ab12_2
+  - libgomp=13.2.0=hf8544c7_2
+  - libstdcxx-devel_linux-aarch64=12.3.0=h8b5ab12_2
+  - libstdcxx-ng=13.2.0=h9a76618_2
+  - mathjax=3.2.2=h8af1aa0_0
+  - pari-elldata=0.0.20161017=0
+  - pari-galdata=0.0.20180411=0
+  - pari-galpol=0.0.20180625=0
+  - pari-seadata-small=0.0.20090618=0
+  - python_abi=3.10=4_cp310
+  - tzdata=2023c=h71feb2d_0
+  - fonts-conda-forge=1=0
+  - pari-seadata=0.0.20090618=0
+  - sysroot_linux-aarch64=2.17=h5b4a56d_13
+  - binutils_impl_linux-aarch64=2.40=h870a726_0
+  - fonts-conda-ecosystem=1=0
+  - binutils=2.40=h64c2a2e_0
+  - binutils_linux-aarch64=2.40=h94bbfa1_2
+  - _openmp_mutex=4.5=2_kmp_llvm
+  - libgcc-ng=13.2.0=hf8544c7_2
+  - bc=1.07.1=hf897c2e_0
+  - bdw-gc=8.0.6=hd62202e_0
+  - bzip2=1.0.8=hf897c2e_4
+  - c-ares=1.20.1=h31becfc_0
+  - cliquer=1.22=hb9de7d4_0
+  - gengetopt=2.23=h01db608_0
+  - gf2x=1.3.0=h1b3b3a3_2
+  - giflib=5.2.1=hb4cce97_3
+  - gmp=6.2.1=h7fd3ca4_0
+  - icu=72.1=hcf00150_0
+  - jpeg=9e=h2a766a3_3
+  - keyutils=1.6.1=h4e544f5_0
+  - lerc=4.0.0=h4de3ea5_0
+  - libatomic_ops=7.6.14=h4e544f5_0
+  - libbraiding=1.1=h7fd3ca4_0
+  - libdeflate=1.17=hb4cce97_0
+  - libev=4.33=h516909a_1
+  - libexpat=2.5.0=hd600fc2_1
+  - libffi=3.4.2=h3557bc0_5
+  - libgfortran5=13.2.0=h582850c_2
+  - libiconv=1.17=h9cdd2b7_0
+  - libnsl=2.0.0=h31becfc_1
+  - libsanitizer=12.3.0=h8ebda82_2
+  - libsodium=1.0.18=hb9de7d4_1
+  - libtool=2.4.7=h4de3ea5_0
+  - libuuid=2.38.1=hb4cce97_0
+  - libuv=1.46.0=h31becfc_0
+  - libwebp-base=1.2.4=h4e544f5_0
+  - libzlib=1.2.13=h31becfc_5
+  - lrcalc=2.1=h4de3ea5_5
+  - m4=1.4.18=h516909a_1001
+  - make=4.3=h309ac5b_1
+  - metis=5.1.0=h2f0025b_1007
+  - nauty=2.7.2=hf897c2e_0
+  - ncurses=6.4=h2e1726e_0
+  - ninja=1.11.1=hdd96247_0
+  - openssl=3.1.3=h31becfc_0
+  - palp=2.20=hb9de7d4_0
+  - patch=2.7.6=hf897c2e_1002
+  - pkg-config=0.29.2=hb9de7d4_1008
+  - planarity=3.0.0.5=hb9de7d4_1002
+  - primesieve=11.1=h2f0025b_0
+  - qhull=2020.2=hd62202e_2
+  - rhash=1.4.4=h31becfc_0
+  - symmetrica=3.0.1=hd600fc2_0
+  - xz=5.2.6=h9cdd2b7_0
+  - cddlib=1!0.94m=h719063d_0
+  - ecm=7.0.4=h719063d_1002
+  - expat=2.5.0=hd600fc2_1
+  - gcc_impl_linux-aarch64=12.3.0=hcde2664_2
+  - givaro=4.1.1=h192cbe9_1
+  - glpk=5.0=h66325d0_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libgfortran-ng=13.2.0=he9431aa_2
+  - libhomfly=1.02r6=hb9de7d4_0
+  - libnghttp2=1.52.0=h250e5c5_0
+  - libpng=1.6.39=hf9034f9_0
+  - libsqlite=3.43.0=h194ca79_0
+  - libssh2=1.11.0=h492db2e_0
+  - libxml2=2.10.4=h430b14f_0
+  - mpfr=4.2.0=h96f194b_0
+  - ntl=11.4.3=h0d7519b_1
+  - perl=5.32.1=4_h31becfc_perl5
+  - primecount=7.9=hd600fc2_0
+  - readline=8.2=h8fc344f_1
+  - tar=1.34=h048efde_0
+  - tk=8.6.13=h194ca79_0
+  - zeromq=4.3.4=h01db608_1
+  - zlib=1.2.13=h31becfc_5
+  - zstd=1.5.5=h4c53e97_0
+  - autoconf=2.71=pl5321h2148fe1_1
+  - ecl=21.2.1=haa44c19_2
+  - freetype=2.12.1=hf0a5ef3_2
+  - gcc=12.3.0=hc1b51f9_2
+  - gcc_linux-aarch64=12.3.0=h464a8f7_2
+  - gfan=0.6.2=h5f589ec_1003
+  - gfortran_impl_linux-aarch64=12.3.0=hb7244be_2
+  - gxx_impl_linux-aarch64=12.3.0=hcde2664_2
+  - krb5=1.21.2=hc419048_0
+  - libboost=1.82.0=hbfc56d7_2
+  - libflint=2.9.0=hd3470fa_ntl_100
+  - libhwloc=2.9.1=h21e8147_0
+  - libopenblas=0.3.23=pthreads_hd703e6f_0
+  - libtiff=4.5.0=h4c1066a_2
+  - llvm-openmp=17.0.2=h8b0cb96_0
+  - m4ri=20140914=h75e8696_1005
+  - mpc=1.3.1=hf4c8f4c_0
+  - mpfi=1.5.4=h846f343_1001
+  - pari=2.15.4=h169c2a7_2_pthread
+  - ppl=1.2=h984aac9_1006
+  - python=3.10.12=hbbe8eec_0_cpython
+  - qd=2.3.22=h05efe27_1004
+  - sqlite=3.43.0=h3b3482f_0
+  - tachyon=0.99b6=h63ab1d9_1001
+  - texinfo=7.0=pl5321h17f021e_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - arb=2.23.0=h37d5dab_0
+  - automake=1.16.5=pl5321h8af1aa0_0
+  - c-compiler=1.6.0=h31becfc_0
+  - cachetools=5.3.1=pyhd8ed1ab_0
+  - chardet=5.2.0=py310hbbe02a8_1
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - distlib=0.3.7=pyhd8ed1ab_0
+  - eclib=20230424=h0bc7b0f_0
+  - filelock=3.12.4=pyhd8ed1ab_0
+  - fontconfig=2.14.2=ha9a116f_0
+  - fplll=5.4.4=h5cd656c_0
+  - gfortran=12.3.0=h8d4031d_2
+  - gfortran_linux-aarch64=12.3.0=h1993883_2
+  - gxx=12.3.0=hc1b51f9_2
+  - gxx_linux-aarch64=12.3.0=h21accf6_2
+  - lcalc=2.0.5=h3264cc0_1
+  - libblas=3.9.0=17_linuxaarch64_openblas
+  - libboost-devel=1.82.0=h37bb5a9_2
+  - libbrial=1.2.12=h17533bf_1
+  - libcurl=8.3.0=h4e8248e_0
+  - libwebp=1.2.4=h7bdf6e5_1
+  - m4rie=20150908=h75e8696_1001
+  - maxima=5.45.0=haa44c19_3
+  - openblas=0.3.23=pthreads_hef96516_0
+  - packaging=23.2=pyhd8ed1ab_0
+  - pluggy=1.3.0=pyhd8ed1ab_0
+  - singular=4.2.1.p3=h3d4c4c6_2
+  - sympow=2.023.6=h157afb5_3
+  - tbb=2021.9.0=h4c384f3_0
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - typing_extensions=4.8.0=pyha770c72_0
+  - zipp=3.17.0=pyhd8ed1ab_0
+  - boost-cpp=1.82.0=h62f3a30_2
+  - brial=1.2.12=pyh694c41f_1
+  - cmake=3.27.6=hef020d8_0
+  - curl=8.3.0=h4e8248e_0
+  - cxx-compiler=1.6.0=h2a328a1_0
+  - fortran-compiler=1.6.0=h7048d53_0
+  - importlib-metadata=6.8.0=pyha770c72_0
+  - libcblas=3.9.0=17_linuxaarch64_openblas
+  - libgd=2.3.3=h5fc1a20_5
+  - liblapack=3.9.0=17_linuxaarch64_openblas
+  - pyproject-api=1.6.1=pyhd8ed1ab_0
+  - typing-extensions=4.8.0=hd8ed1ab_0
+  - arpack=3.7.0=hf862f49_2
+  - compilers=1.6.0=h8af1aa0_0
+  - fflas-ffpack=2.4.3=hf104d39_2
+  - gsl=2.7=h294027d_0
+  - iml=1.0.5=h9076c59_1003
+  - importlib_metadata=6.8.0=hd8ed1ab_0
+  - liblapacke=3.9.0=17_linuxaarch64_openblas
+  - platformdirs=3.11.0=pyhd8ed1ab_0
+  - suitesparse=5.10.1=h1404dd6_1
+  - blas-devel=3.9.0=17_linuxaarch64_openblas
+  - giac=1.9.0.21=h04922a4_1
+  - igraph=0.9.10=hefb87a8_1
+  - linbox=1.6.3=h31716a8_7
+  - virtualenv=20.24.4=pyhd8ed1ab_0
+  - blas=2.117=openblas
+  - rw=0.9=hf897c2e_0
+  - tox=4.11.3=pyhd8ed1ab_0