update lock files

Author: tobiasdiez

.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": {

.github/workflows/conda-lock-update.ps1

@@ -0,0 +1,32 @@
+#!/usr/bin/env pwsh
+
+$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Path
+$rootDir = Join-Path -Path $scriptDir -ChildPath ..\..\
+
+& "$rootDir/bootstrap-conda"
+
+$platforms = @{
+    "linux-64" = "linux"
+    "osx-64" = "macos"
+}
+$pythons = "3.9", "3.10", "3.11"
+$tags = "", "-dev"
+$sources = "", "src"
+
+foreach ($platform in $platforms.GetEnumerator()) {
+    foreach ($python in $pythons) {
+        foreach ($tag in $tags) {
+            foreach ($src in $sources) {
+                $envFile = Join-Path -Path $rootDir -ChildPath "$src\environment$tag-$python.yml"
+                $lockFile = Join-Path -Path $rootDir -ChildPath "$src\environment$tag-$python-$($platform.Value)"
+
+                if (-not (Test-Path $envFile)) {
+                    continue
+                }
+
+                echo "Updating lock file for $envFile at $lockFile"
+                & "conda-lock" --channel conda-forge --kind env --platform $platform.Key --file $envFile --lockfile $lockFile --filename-template $lockFile
+            }
+        }
+    }
+}

.vscode/settings.json

@@ -34,5 +34,6 @@
         "sagemath",
         "Cython"
     ],
-    "editor.formatOnType": true
+    "editor.formatOnType": true,
+    "esbonio.sphinx.confDir": ""
 }

bootstrap-conda

@@ -152,5 +152,6 @@ for python_version in 3.9 3.10 3.11; do
                 done
             fi
         done
-    ) 4>> src/environment-dev-$python_version.yml 5>> src/environment-optional-$python_version.yml
+    #) 4>> src/environment-dev-$python_version.yml 5>> src/environment-optional-$python_version.yml
+    ) 4>> /dev/null 5>> src/environment-optional-$python_version.yml
 done

build/pkgs/_prereq/distros/conda.txt

@@ -1,7 +1,8 @@
-compilers
-make
-m4
-perl
-python
-tar
-bc
+# Not needed on conda
+#compilers
+#make
+#m4
+#perl
+#python
+#tar
+#bc

build/pkgs/patchelf/distros/conda.txt

@@ -1 +1,2 @@
-patchelf
+# Not available on macos
+# patchelf

environment-3.10-linux.yml

@@ -1,52 +1,46 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 3e531235a513060f63b991c223aa35c0cb0c16aef417e93c3df677572197bc24
+# input_hash: 722f5cecf921eb12ba9c645f0b616fed4ffaff10b7e29c286b3a70f8df40a036
 
 channels:
   - conda-forge
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
-  - _r-mutex=1.0.1=anacondar_1
   - ca-certificates=2023.7.22=hbcca054_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-64=2.6.32=he073ed8_16
   - ld_impl_linux-64=2.40=h41732ed_0
-  - libgcc-devel_linux-64=12.3.0=h8bca6fd_0
-  - libgfortran5=13.1.0=h15d22d2_0
-  - libstdcxx-devel_linux-64=12.3.0=h8bca6fd_0
-  - libstdcxx-ng=13.1.0=hfd8a6a1_0
+  - libboost-headers=1.82.0=ha770c72_2
+  - libgcc-devel_linux-64=12.3.0=h8bca6fd_2
+  - libstdcxx-ng=13.2.0=h7e041cc_2
+  - mathjax=3.2.2=ha770c72_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=3.11=3_cp311
+  - python_abi=3.10=4_cp310
   - tzdata=2023c=h71feb2d_0
   - fonts-conda-forge=1=0
-  - libgfortran-ng=13.1.0=h69a702a_0
-  - libgomp=13.1.0=he5830b7_0
+  - libgomp=13.2.0=h807b86a_2
   - pari-seadata=0.0.20090618=0
   - sysroot_linux-64=2.12=he073ed8_16
   - binutils_impl_linux-64=2.40=hf600244_0
   - fonts-conda-ecosystem=1=0
   - binutils=2.40=hdd6e379_0
-  - binutils_linux-64=2.40=hbdbef99_1
+  - binutils_linux-64=2.40=hbdbef99_2
   - _openmp_mutex=4.5=2_kmp_llvm
-  - libgcc-ng=13.1.0=he5830b7_0
-  - bc=1.07.1=h7f98852_0
+  - libgcc-ng=13.2.0=h807b86a_2
   - bdw-gc=8.0.6=h4bd325d_0
   - bzip2=1.0.8=h7f98852_4
   - c-ares=1.19.1=hd590300_0
   - cliquer=1.22=h36c2ea0_0
-  - fribidi=1.0.10=h36c2ea0_0
   - gengetopt=2.23=h9c3ff4c_0
-  - gettext=0.21.1=h27087fc_0
   - gf2x=1.3.0=ha476b99_2
   - giflib=5.2.1=h0b41bf4_3
   - gmp=6.2.1=h58526e2_0
-  - graphite2=1.3.13=h58526e2_1001
   - icu=72.1=hcb278e6_0
   - keyutils=1.6.1=h166bdaf_0
   - lerc=4.0.0=h27087fc_0
@@ -56,171 +50,134 @@ dependencies:
   - libev=4.33=h516909a_1
   - libexpat=2.5.0=hcb278e6_1
   - libffi=3.4.2=h7f98852_5
+  - libgfortran5=13.2.0=ha4646dd_2
   - libiconv=1.17=h166bdaf_0
-  - libjpeg-turbo=2.1.5.1=h0b41bf4_0
-  - libnsl=2.0.0=h7f98852_0
-  - libopenblas=0.3.23=pthreads_h80387f5_0
-  - libsanitizer=12.3.0=h0f45ef3_0
+  - libjpeg-turbo=2.1.5.1=hd590300_1
+  - libnsl=2.0.0=hd590300_1
+  - libsanitizer=12.3.0=h0f45ef3_2
   - libsodium=1.0.18=h36c2ea0_1
   - libtool=2.4.7=h27087fc_0
   - libuuid=2.38.1=h0b41bf4_0
-  - libuv=1.44.2=h166bdaf_0
+  - libuv=1.46.0=hd590300_0
   - libwebp-base=1.3.1=hd590300_0
   - libzlib=1.2.13=hd590300_5
   - lrcalc=2.1=h27087fc_5
   - m4=1.4.18=h516909a_1001
-  - make=4.3=hd18ef5c_1
-  - metis=5.1.1=h59595ed_0
+  - metis=5.1.0=h59595ed_1007
   - nauty=2.7.2=h7f98852_0
   - ncurses=6.4=hcb278e6_0
   - ninja=1.11.1=h924138e_0
-  - openssl=3.1.1=hd590300_1
+  - openssl=3.1.3=hd590300_0
   - palp=2.20=h36c2ea0_0
   - patch=2.7.6=h7f98852_1002
-  - pixman=0.40.0=h36c2ea0_0
   - pkg-config=0.29.2=h36c2ea0_1008
   - planarity=3.0.0.5=h36c2ea0_1002
   - primesieve=11.1=h59595ed_0
-  - pthread-stubs=0.4=h36c2ea0_1001
-  - qd=2.3.22=h2cc385e_1004
   - qhull=2020.2=h4bd325d_2
-  - rhash=1.4.3=h166bdaf_0
-  - sed=4.8=he412f7d_0
+  - rhash=1.4.4=hd590300_0
   - symmetrica=3.0.1=hcb278e6_0
-  - xorg-kbproto=1.0.7=h7f98852_1002
-  - xorg-libice=1.0.10=h7f98852_0
-  - xorg-libxau=1.0.11=hd590300_0
-  - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xorg-renderproto=0.11.1=h7f98852_1002
-  - xorg-xextproto=7.3.0=h0b41bf4_1003
-  - xorg-xproto=7.0.31=h7f98852_1007
+  - tbb=2021.7.0=h924138e_0
   - xz=5.2.6=h166bdaf_0
   - cddlib=1!0.94m=h9202a9a_0
   - ecm=7.0.4=h9202a9a_1002
   - expat=2.5.0=hcb278e6_1
-  - gcc_impl_linux-64=12.3.0=he2b93b0_0
+  - gcc_impl_linux-64=12.3.0=he2b93b0_2
   - givaro=4.1.1=h192cbe9_1
   - glpk=5.0=h445213a_0
-  - libblas=3.9.0=17_linux64_openblas
   - libedit=3.1.20191231=he28a2e2_2
+  - libgfortran-ng=13.2.0=h69a702a_2
   - libhomfly=1.02r6=h36c2ea0_0
   - libnghttp2=1.52.0=h61bc06f_0
   - libpng=1.6.39=h753d276_0
-  - libsqlite=3.42.0=h2797004_0
+  - libsqlite=3.43.0=h2797004_0
   - libssh2=1.11.0=h0841786_0
-  - libxcb=1.15=h0b41bf4_0
   - libxml2=2.10.4=hfdac1af_0
   - mpfr=4.2.0=hb012696_0
   - ntl=11.4.3=hef3c4d3_1
-  - openblas=0.3.23=pthreads_h855a84d_0
-  - pcre2=10.40=hc3806b6_0
   - perl=5.32.1=4_hd590300_perl5
   - primecount=7.9=hcb278e6_0
   - readline=8.2=h8228510_1
-  - tar=1.34=hb2e2bae_1
-  - tk=8.6.12=h27826a3_0
-  - xorg-libsm=1.2.3=hd9c2040_1000
+  - tk=8.6.13=h2797004_0
   - zeromq=4.3.4=h9c3ff4c_1
   - zlib=1.2.13=hd590300_5
-  - zstd=1.5.2=hfc55251_7
+  - zstd=1.5.5=hfc55251_0
   - autoconf=2.71=pl5321h2b4cb7a_1
-  - boost-cpp=1.82.0=he19a28c_1
-  - bwidget=1.9.14=ha770c72_1
   - ecl=21.2.1=h9d73b02_2
-  - fplll=5.4.4=h8780c30_0
-  - freetype=2.12.1=hca18f0e_1
-  - gcc=12.3.0=h8d2909c_1
-  - gcc_linux-64=12.3.0=h76fc315_1
+  - freetype=2.12.1=h267a509_2
+  - gcc=12.3.0=h8d2909c_2
+  - gcc_linux-64=12.3.0=h76fc315_2
   - gfan=0.6.2=hb86e20a_1003
-  - gfortran_impl_linux-64=12.3.0=hfcedea8_0
-  - gxx_impl_linux-64=12.3.0=he2b93b0_0
-  - krb5=1.20.1=h81ceb04_0
-  - libcblas=3.9.0=17_linux64_openblas
+  - gfortran_impl_linux-64=12.3.0=hfcedea8_2
+  - krb5=1.21.2=h659d440_0
+  - libboost=1.82.0=h1bacd13_2
   - libflint=2.9.0=h2f819a4_ntl_100
-  - libglib=2.76.4=hebfc3b9_0
-  - libhwloc=2.9.1=hd6dc26d_0
-  - liblapack=3.9.0=17_linux64_openblas
-  - libtiff=4.5.1=h8b53f26_0
-  - llvm-openmp=16.0.6=h4dfa4b3_0
+  - libopenblas=0.3.24=pthreads_h413a1c8_0
+  - libtiff=4.5.1=h8b53f26_1
+  - llvm-openmp=17.0.2=h4dfa4b3_0
   - m4ri=20140914=h7ca028e_1005
   - mpc=1.3.1=hfe3b2da_0
   - mpfi=1.5.4=h9f54685_1001
   - pari=2.15.4=h4d4ae9b_2_pthread
   - ppl=1.2=h6ec01c2_1006
-  - python=3.11.4=hab00c5b_0_cpython
-  - sqlite=3.42.0=h2c6b66d_0
+  - python=3.10.12=hd12c33a_0_cpython
+  - qd=2.3.22=h2cc385e_1004
+  - sqlite=3.43.0=h2c6b66d_0
   - tachyon=0.99b6=0
   - texinfo=7.0=pl5321h0f457ee_0
-  - tktable=2.10=hb7b940f_3
-  - xorg-libx11=1.8.6=h8ee46fc_0
   - appdirs=1.4.4=pyh9f0ad1d_0
   - arb=2.23.0=h44d021b_0
-  - arpack=3.7.0=hdefa2d7_2
   - automake=1.16.5=pl5321ha770c72_0
   - c-compiler=1.6.0=hd590300_0
   - cachetools=5.3.1=pyhd8ed1ab_0
-  - chardet=5.1.0=py311h38be061_0
+  - chardet=5.2.0=py310hff52083_1
   - colorama=0.4.6=pyhd8ed1ab_0
   - distlib=0.3.7=pyhd8ed1ab_0
   - eclib=20230424=hdef1efb_0
-  - fflas-ffpack=2.4.3=h912ac81_2
-  - filelock=3.12.2=pyhd8ed1ab_0
+  - filelock=3.12.4=pyhd8ed1ab_0
   - fontconfig=2.14.2=h14ed4e7_0
-  - gfortran=12.3.0=h499e0f7_1
-  - gfortran_linux-64=12.3.0=h7fe76b4_1
-  - gsl=2.7=he838d99_0
-  - gxx=12.3.0=h8d2909c_1
-  - gxx_linux-64=12.3.0=h8a814eb_1
-  - iml=1.0.5=hd75c201_1003
+  - fplll=5.4.4=h8780c30_0
+  - gfortran=12.3.0=h499e0f7_2
+  - gfortran_linux-64=12.3.0=h7fe76b4_2
   - lcalc=2.0.5=h6a8a7c6_1
-  - libbrial=1.2.12=h138cd66_0
-  - libcurl=8.1.2=h409715c_0
-  - liblapacke=3.9.0=17_linux64_openblas
+  - libblas=3.9.0=18_linux64_openblas
+  - libboost-devel=1.82.0=h00ab1b0_2
+  - libbrial=1.2.12=h3155cbd_1
+  - libcurl=8.3.0=hca28451_0
   - libwebp=1.3.1=hbf2b3c1_0
   - m4rie=20150908=h7ca028e_1001
-  - markupsafe=2.1.3=py311h459d7ec_0
   - maxima=5.45.0=h9d73b02_3
-  - packaging=23.1=pyhd8ed1ab_0
-  - pluggy=1.2.0=pyhd8ed1ab_0
-  - pycparser=2.21=pyhd8ed1ab_0
-  - pytz=2023.3=pyhd8ed1ab_0
-  - simplegeneric=0.8.1=py_1
+  - openblas=0.3.24=pthreads_h7a3da1a_0
+  - packaging=23.2=pyhd8ed1ab_0
+  - pluggy=1.3.0=pyhd8ed1ab_0
   - singular=4.2.1.p3=h1ea75ed_2
   - sympow=2.023.6=hc6ab17c_3
-  - tbb=2021.9.0=hf52228f_0
-  - toml=0.10.2=pyhd8ed1ab_0
   - tomli=2.0.1=pyhd8ed1ab_0
-  - typing_extensions=4.7.1=pyha770c72_0
-  - tzlocal=5.0.1=py311h38be061_0
-  - xorg-libxext=1.3.4=h0b41bf4_2
-  - xorg-libxrender=0.9.11=hd590300_0
-  - xorg-libxt=1.3.0=hd590300_0
-  - zipp=3.16.2=pyhd8ed1ab_0
-  - blas-devel=3.9.0=17_linux64_openblas
-  - brial=1.2.12=pyha3edaa6_0
-  - cairo=1.16.0=hbbf8b49_1016
-  - cffi=1.15.1=py311h409f033_3
-  - cmake=3.26.4=hcfe8598_0
-  - curl=8.1.2=h409715c_0
-  - cxx-compiler=1.6.0=h00ab1b0_0
+  - typing_extensions=4.8.0=pyha770c72_0
+  - zipp=3.17.0=pyhd8ed1ab_0
+  - boost-cpp=1.82.0=h789c474_2
+  - brial=1.2.12=pyh694c41f_1
+  - cmake=3.27.6=hcfe8598_0
+  - curl=8.3.0=hca28451_0
   - fortran-compiler=1.6.0=heb67821_0
-  - giac=1.9.0.21=h673759e_1
   - importlib-metadata=6.8.0=pyha770c72_0
-  - jinja2=3.1.2=pyhd8ed1ab_1
+  - libcblas=3.9.0=18_linux64_openblas
   - libgd=2.3.3=hfa28ad5_6
-  - linbox=1.6.3=h9d78c56_7
-  - pyproject-api=1.5.3=pyhd8ed1ab_0
+  - liblapack=3.9.0=18_linux64_openblas
+  - pyproject-api=1.6.1=pyhd8ed1ab_0
+  - typing-extensions=4.8.0=hd8ed1ab_0
+  - arpack=3.7.0=hdefa2d7_2
+  - fflas-ffpack=2.4.3=h912ac81_2
+  - gsl=2.7=he838d99_0
+  - iml=1.0.5=hd75c201_1003
+  - importlib_metadata=6.8.0=hd8ed1ab_0
+  - liblapacke=3.9.0=18_linux64_openblas
+  - platformdirs=3.11.0=pyhd8ed1ab_0
   - suitesparse=5.10.1=h9e50725_1
-  - typing-extensions=4.7.1=hd8ed1ab_0
-  - blas=2.117=openblas
-  - compilers=1.6.0=ha770c72_0
-  - harfbuzz=7.3.0=hdb3a94d_0
+  - blas-devel=3.9.0=18_linux64_openblas
+  - giac=1.9.0.21=h673759e_1
   - igraph=0.9.10=ha1f048c_1
-  - importlib_metadata=6.8.0=hd8ed1ab_0
-  - platformdirs=3.9.1=pyhd8ed1ab_0
-  - pango=1.50.14=heaa33ce_1
+  - linbox=1.6.3=h9d78c56_7
+  - virtualenv=20.24.4=pyhd8ed1ab_0
+  - blas=2.118=openblas
   - rw=0.9=h7f98852_0
-  - virtualenv=20.24.1=pyhd8ed1ab_0
-  - r-base=4.3.0=h0fc540b_0
-  - tox=4.6.4=pyhd8ed1ab_0
-  - rpy2=3.5.11=py311r43h1f0f07a_2
+  - tox=4.11.3=pyhd8ed1ab_0