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Remediate the emSign CA incident - #11

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Thomas A Caswell (tacaswell) wants to merge 3 commits into
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tacaswell:emSign
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Thomas A Caswell (tacaswell) wants to merge 3 commits into
NSLS2:mainfrom
tacaswell:emSign

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Update locked packages and GitHub Actions to versions fixed for the emSign CA incident.

  • Require Pixi >= 0.82.1
    Pixi 0.82.1 is the release fixed for the emSign CA incident.
    • pixi.toml: requires-pixi None -> '>=0.82.1' (added)
  • Update ca-certificates, certifi, pip in pixi.lock
    Update the locked packages to versions fixed for the emSign CA incident.
    Raise the floors in pixi.toml:
    • dependencies.pip: '>=25.2,<26' -> '>=26.2.2' (dropped the upper bound <26, which excluded the fixed version)
      Output of pixi update --manifest-path pixi.toml ca-certificates certifi pip:
      (output omitted here to keep the description short; it is in the commit message)
  • Update GitHub Actions for the emSign CA incident
    • .github/workflows/ci.yaml:33: prefix-dev/setup-pixi pixi-version v0.74.0 -> v0.83.0
    • .github/workflows/ci.yaml:54: prefix-dev/setup-pixi pixi-version v0.74.0 -> v0.83.0
    • .github/workflows/docs.yml:38: prefix-dev/setup-pixi pixi-version v0.74.0 -> v0.83.0

Pixi 0.82.1 is the release fixed for the emSign CA incident.
- pixi.toml: requires-pixi None -> '>=0.82.1' (added)
Update the locked packages to versions fixed for the emSign CA incident.

Raise the floors in pixi.toml:
- dependencies.pip: '>=25.2,<26' -> '>=26.2.2' (dropped the upper bound <26, which excluded the fixed version)

Output of `pixi update --manifest-path pixi.toml ca-certificates certifi pip`:

     ╭─ Running build for recipe: gsas-ii-2.0.0-hb0f4dca_0
     │
     │ ╭─ Fetching source code
     │ │ No sources to fetch
     │ │
     │ ╰─────────────────── (took 0 seconds)
     │
     │ ╭─ Externally resolved dependencies recipe: gsas-ii-2.0.0-hb0f4dca_0
     │ │
     │ │ Resolved build dependencies(gsas-ii-2.0.0-hb0f4dca_0):
     │ │ ╭─────────┬──────┬─────────┬───────┬─────────┬──────╮
     │ │ │ Package ┆ Spec ┆ Version ┆ Build ┆ Channel ┆ Size │
     │ │ ╞═════════╪══════╪═════════╪═══════╪═════════╪══════╡
     │ │ ╰─────────┴──────┴─────────┴───────┴─────────┴──────╯
     │ │ Resolved host dependencies(gsas-ii-2.0.0-hb0f4dca_0):
     │ │ ╭──────────────────────────┬──────────────────────────────────┬────────────┬──────────────────────┬─────────────┬────────────╮
     │ │ │ Package                  ┆ Spec                             ┆ Version    ┆ Build                ┆ Channel     ┆       Size │
     │ │ ╞══════════════════════════╪══════════════════════════════════╪════════════╪══════════════════════╪═════════════╪════════════╡
     │ │ │ cython                   ┆ cython >=3.0.11,<4               ┆ 3.2.9      ┆ py313hc80a56d_0      ┆ conda-forge ┆   3.59 MiB │
     │ │ │ gcc                      ┆ gcc                              ┆ 16.1.0     ┆ hc6a0c74_2           ┆ conda-forge ┆  28.58 KiB │
     │ │ │ gfortran                 ┆ gfortran                         ┆ 16.1.0     ┆ hc6a0c74_2           ┆ conda-forge ┆  28.06 KiB │
     │ │ │ meson-python             ┆ meson-python >=0.17.1,<0.18      ┆ 0.17.1     ┆ pyh70fd9c4_1         ┆ conda-forge ┆  72.53 KiB │
     │ │ │ ninja                    ┆ ninja >=1.12.1,<2                ┆ 1.13.2     ┆ h171cf75_1           ┆ conda-forge ┆ 182.39 KiB │
     │ │ │ numpy                    ┆ numpy >=2.2.1,<2.5.0             ┆ 2.4.6      ┆ py313hf6604e3_0      ┆ conda-forge ┆   8.45 MiB │
     │ │ │ pip                      ┆ pip >=24.3.1,<25                 ┆ 24.3.1     ┆ pyh145f28c_2         ┆ conda-forge ┆   1.18 MiB │
     │ │ │ pkg-config               ┆ pkg-config >=0.29.2,<0.30        ┆ 0.29.2     ┆ h7c397b8_1011        ┆ conda-forge ┆ 137.70 KiB │
     │ │ │ pyproject-metadata       ┆ pyproject-metadata >=0.9.0,<0.10 ┆ 0.9.1      ┆ pyhd8ed1ab_0         ┆ conda-forge ┆  21.47 KiB │
     │ │ │ python                   ┆ python >=3.10,<3.14              ┆ 3.13.15    ┆ hb101c97_101_cp313   ┆ conda-forge ┆  35.75 MiB │
     │ │ │ tomli                    ┆ tomli >=2.2.1,<3                 ┆ 2.4.1      ┆ pyhcf101f3_0         ┆ conda-forge ┆  21.06 KiB │
     │ │ │ wheel                    ┆ wheel >=0.45.1,<0.46             ┆ 0.45.1     ┆ pyhd8ed1ab_1         ┆ conda-forge ┆  61.46 KiB │
     │ │ │ _openmp_mutex            ┆                                  ┆ 4.5        ┆ 20_gnu               ┆ conda-forge ┆  28.27 KiB │
     │ │ │ binutils_impl_linux-64   ┆                                  ┆ 2.46.1     ┆ default_hfdba357_102 ┆ conda-forge ┆   3.54 MiB │
     │ │ │ bzip2                    ┆                                  ┆ 1.0.8      ┆ hda65f42_10          ┆ conda-forge ┆ 251.77 KiB │
     │ │ │ ca-certificates          ┆                                  ┆ 2026.10.19 ┆ hbd8a1cb_0           ┆ conda-forge ┆ 128.32 KiB │
     │ │ │ conda-gcc-specs          ┆                                  ┆ 16.1.0     ┆ h5a3cd76_2           ┆ conda-forge ┆  31.63 KiB │
     │ │ │ gcc_impl_linux-64        ┆                                  ┆ 16.1.0     ┆ hceef32b_2           ┆ conda-forge ┆  81.09 MiB │
     │ │ │ gfortran_impl_linux-64   ┆                                  ┆ 16.1.0     ┆ h08e1a1a_2           ┆ conda-forge ┆  20.05 MiB │
     │ │ │ icu                      ┆                                  ┆ 78.3       ┆ py310h44b86e0_2      ┆ conda-forge ┆  13.79 MiB │
     │ │ │ kernel-headers_linux-64  ┆                                  ┆ 4.18.0     ┆ he073ed8_9           ┆ conda-forge ┆   1.22 MiB │
     │ │ │ ld_impl_linux-64         ┆                                  ┆ 2.46.1     ┆ default_hbd61a6d_102 ┆ conda-forge ┆ 727.83 KiB │
     │ │ │ libblas                  ┆                                  ┆ 3.11.0     ┆ 9_h4a7cf45_openblas  ┆ conda-forge ┆  17.61 KiB │
     │ │ │ libcblas                 ┆                                  ┆ 3.11.0     ┆ 9_h0358290_openblas  ┆ conda-forge ┆  17.58 KiB │
     │ │ │ libexpat                 ┆                                  ┆ 2.8.1      ┆ hecca717_1           ┆ conda-forge ┆  76.03 KiB │
     │ │ │ libffi                   ┆                                  ┆ 3.7.0      ┆ h3435931_0           ┆ conda-forge ┆  65.99 KiB │
     │ │ │ libgcc                   ┆                                  ┆ 16.1.0     ┆ ha9f2e26_2           ┆ conda-forge ┆   1.01 MiB │
     │ │ │ libgcc-devel_linux-64    ┆                                  ┆ 16.1.0     ┆ h59071f9_102         ┆ conda-forge ┆   2.96 MiB │
     │ │ │ libgfortran              ┆                                  ┆ 16.1.0     ┆ h69a702a_2           ┆ conda-forge ┆  27.59 KiB │
     │ │ │ libgfortran5             ┆                                  ┆ 16.1.0     ┆ h79bb938_2           ┆ conda-forge ┆   2.42 MiB │
     │ │ │ libgomp                  ┆                                  ┆ 16.1.0     ┆ he0feb66_2           ┆ conda-forge ┆ 625.46 KiB │
     │ │ │ liblapack                ┆                                  ┆ 3.11.0     ┆ 9_h47877c9_openblas  ┆ conda-forge ┆  17.60 KiB │
     │ │ │ liblzma                  ┆                                  ┆ 5.8.3      ┆ hb03c661_1           ┆ conda-forge ┆ 110.35 KiB │
     │ │ │ libmpdec                 ┆                                  ┆ 4.0.0      ┆ hb03c661_2           ┆ conda-forge ┆  90.58 KiB │
     │ │ │ libopenblas              ┆                                  ┆ 0.3.34     ┆ pthreads_h94d23a6_0  ┆ conda-forge ┆   5.68 MiB │
     │ │ │ libsanitizer             ┆                                  ┆ 16.1.0     ┆ hf2715c6_2           ┆ conda-forge ┆   7.59 MiB │
     │ │ │ libsqlite                ┆                                  ┆ 3.53.4     ┆ h13e7031_1           ┆ conda-forge ┆ 951.51 KiB │
     │ │ │ libstdcxx                ┆                                  ┆ 16.1.0     ┆ h934c35e_2           ┆ conda-forge ┆   6.32 MiB │
     │ │ │ libstdcxx-devel_linux-64 ┆                                  ┆ 16.1.0     ┆ h41cdd0d_102         ┆ conda-forge ┆  22.39 MiB │
     │ │ │ libuuid                  ┆                                  ┆ 2.42.2     ┆ h5347b49_0           ┆ conda-forge ┆  39.08 KiB │
     │ │ │ libzlib                  ┆                                  ┆ 1.3.2      ┆ h25fd6f3_3           ┆ conda-forge ┆  62.22 KiB │
     │ │ │ meson                    ┆                                  ┆ 1.12.0     ┆ pyhcf101f3_0         ┆ conda-forge ┆ 777.97 KiB │
     │ │ │ ncurses                  ┆                                  ┆ 6.6        ┆ hdb14827_1           ┆ conda-forge ┆ 889.84 KiB │
     │ │ │ openssl                  ┆                                  ┆ 3.6.3      ┆ h35e630c_1           ┆ conda-forge ┆   3.03 MiB │
     │ │ │ packaging                ┆                                  ┆ 26.3       ┆ pyhc364b38_0         ┆ conda-forge ┆ 113.64 KiB │
     │ │ │ python_abi               ┆                                  ┆ 3.13       ┆ 8_cp313              ┆ conda-forge ┆   6.84 KiB │
     │ │ │ readline                 ┆                                  ┆ 8.3        ┆ hd6e31c0_1           ┆ conda-forge ┆ 340.72 KiB │
     │ │ │ sysroot_linux-64         ┆                                  ┆ 2.28       ┆ h4ee821c_9           ┆ conda-forge ┆  22.90 MiB │
     │ │ │ tk                       ┆                                  ┆ 8.6.13     ┆ noxft_hd70dff1_3     ┆ conda-forge ┆   3.39 MiB │
     │ │ │ tzdata                   ┆                                  ┆ 2026c      ┆ h151e31d_0           ┆ conda-forge ┆ 116.06 KiB │
     │ │ │ zstd                     ┆                                  ┆ 1.5.7      ┆ hb78ec9c_7           ┆ conda-forge ┆ 587.21 KiB │
     │ │ ╰──────────────────────────┴──────────────────────────────────┴────────────┴──────────────────────┴─────────────┴────────────╯
     │ │ Resolved run dependencies(gsas-ii-2.0.0-hb0f4dca_0):
     │ │ ╭──────────────────┬───────────────────────────────────────╮
     │ │ │ Name             ┆ Spec                                  │
     │ │ ╞══════════════════╪═══════════════════════════════════════╡
     │ │ │ Run dependencies ┆                                       │
     │ │ │ h5py             ┆ >=3.12.1,<4                           │
     │ │ │ imageio          ┆ >=2.36.1,<3                           │
     │ │ │ libgcc-ng        ┆ *                                     │
     │ │ │ libgfortran5     ┆ *                                     │
     │ │ │ matplotlib-base  ┆ >=3.10.0,<4                           │
     │ │ │ numpy            ┆ >=2.2.1,<2.5.0                        │
     │ │ │                  ┆ >=1.23,<3 (RE of [host: numpy])       │
     │ │ │ pillow           ┆ >=11.1.0,<12                          │
     │ │ │ pybaselines      ┆ >=1.2.0,<2                            │
     │ │ │ pycifrw          ┆ >=4.4.0                               │
     │ │ │ pyopengl         ┆ >=3.1.6,<4                            │
     │ │ │ python           ┆ >=3.10                                │
     │ │ │ python_abi       ┆ 3.13.* *_cp313 (RE of [host: python]) │
     │ │ │ requests         ┆ >=2.32.3,<3                           │
     │ │ │ scipy            ┆ >=1.15.0,<2                           │
     │ │ │ seekpath         ┆ >=2.1.0,<3                            │
     │ │ │ wxpython         ┆ >=4.2.2,<5                            │
     │ │ │ xmltodict        ┆ >=0.14.2,<0.15                        │
     │ │ │ zarr             ┆ >=2.18.3,<4                           │
     │ │ ╰──────────────────┴───────────────────────────────────────╯
     │ │
     │ ╰─────────────────── (took 0 seconds)
     │
     │ ╭─ Running build script
     │ │ + $PREFIX/bin/python -m pip install --force-reinstall -vv --no-deps --no-build-isolation --no-index /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5
     │ │ aaabe581fe7dd5/e0910fc1
     │ │ Using pip 24.3.1 from $PREFIX/lib/python3.13/site-packages/pip (python 3.13)
     │ │ Non-user install because user site-packages disabled
     │ │ Ignoring indexes: https://pypi.org/simple
     │ │ Created temporary directory: /tmp/pip-build-tracker-hdmjkcbn
     │ │ Initialized build tracking at /tmp/pip-build-tracker-hdmjkcbn
     │ │ Created build tracker: /tmp/pip-build-tracker-hdmjkcbn
     │ │ Entered build tracker: /tmp/pip-build-tracker-hdmjkcbn
     │ │ Created temporary directory: /tmp/pip-install-_mfbjegu
     │ │ Created temporary directory: /tmp/pip-ephem-wheel-cache-4hskxckz
     │ │ Processing /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1
     │ │   Added file:///home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1 to build tracker '/tmp/pip-build-tracker-hdmjkcbn'
     │ │   Created temporary directory: /tmp/pip-modern-metadata-g6iuj96a
     │ │   Preparing metadata (pyproject.toml): started
     │ │   Running command Preparing metadata (pyproject.toml)
     │ │   + meson setup /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1 /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe
     │ │ 581fe7dd5/e0910fc1/.mesonpy-m6jcm80n -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/tcaswell/.cache/rattler/cache/git-v0/checko
     │ │ uts/c5aaabe581fe7dd5/e0910fc1/.mesonpy-m6jcm80n/meson-python-native-file.ini
     │ │   The Meson build system
     │ │   Version: 1.12.0
     │ │   Source dir: /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1
     │ │   Build dir: /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1/.mesonpy-m6jcm80n
     │ │   Build type: native build
     │ │   Project name: gsas_ii
     │ │   Project version: 2.0.0
     │ │   Fortran compiler for the host machine: gfortran (gcc 16.1.0 "GNU Fortran (conda-forge gcc 16.1.0-2) 16.1.0")
     │ │   Fortran linker for the host machine: gfortran ld.bfd 2.46.1
     │ │   C compiler for the host machine: /usr/bin/ccache cc (gcc 16.1.0 "cc (conda-forge gcc 16.1.0-2) 16.1.0")
     │ │   C linker for the host machine: cc ld.bfd 2.46.1
     │ │   Cython compiler for the host machine: cython (cython 3.2.9)
     │ │   Host machine cpu family: x86_64
     │ │   Host machine cpu: x86_64
     │ │   Library m found: YES
     │ │   ../meson.build:29: WARNING: Consider using the built-in optimization level instead of using "-O2".
     │ │   Program python found: YES ($PREFIX/bin/python)
     │ │   Found pkg-config: YES ($PREFIX/bin/pkg-config) 0.29.2
     │ │   Run-time dependency python found: YES 3.13
     │ │   numpy-config found: YES ($PREFIX/bin/numpy-config) 2.4.6
     │ │   Run-time dependency numpy found: YES 2.4.6
     │ │   Build targets in project: 19
     │ │   gsas_ii 2.0.0
     │ │     User defined options
     │ │       Native files: /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1/.mesonpy-m6jcm80n/meson-python-native-file.ini
     │ │       b_ndebug    : if-release
     │ │       b_vscrt     : md
     │ │       buildtype   : release
     │ │   Found ninja-1.13.2 at $PREFIX/bin/ninja
     │ │   + $PREFIX/bin/ninja
     │ │   [1/134] Scanning target convcell for modules
     │ │   [2/134] Scanning target DIFFaXsubs_lib for modules
     │ │   [3/134] Scanning target pack_f.cpython-313-x86_64-linux-gnu for modules
     │ │   [4/134] Scanning target pyspg.cpython-313-x86_64-linux-gnu for modules
     │ │   [5/134] Scanning target pytexture.cpython-313-x86_64-linux-gnu for modules
     │ │   [6/134] Scanning target powsubs_lib for modules
     │ │   [7/134] Scanning target pypowder.cpython-313-x86_64-linux-gnu for modules
     │ │   [8/134] Scanning target spsubs_lib for modules
     │ │   [9/134] Scanning target histogram2d.cpython-313-x86_64-linux-gnu for modules
     │ │   [10/134] Scanning target NISTlatsubs_lib for modules
     │ │   [11/134] Scanning target texturesubs_lib for modules
     │ │   [12/134] Scanning target LATTIC for modules
     │ │   [13/134] Scanning target unpack_cbf.cpython-313-x86_64-linux-gnu for modules
     │ │   [14/134] Scanning target pydiffax.cpython-313-x86_64-linux-gnu for modules
     │ │   [15/134] Generating dynamic dependency information for target convcell
     │ │   [16/134] Generating dynamic dependency information for target DIFFaXsubs_lib
     │ │   [17/134] Generating dynamic dependency information for target powsubs_lib
     │ │   [18/134] Generating dynamic dependency information for target pypowder.cpython-313-x86_64-linux-gnu
     │ │   [19/134] Generating dynamic dependency information for target pack_f.cpython-313-x86_64-linux-gnu
     │ │   [20/134] Generating dynamic dependency information for target histogram2d.cpython-313-x86_64-linux-gnu
     │ │   [21/134] Generating dynamic dependency information for target spsubs_lib
     │ │   [22/134] Generating dynamic dependency information for target pyspg.cpython-313-x86_64-linux-gnu
     │ │   [23/134] Generating dynamic dependency information for target pydiffax.cpython-313-x86_64-linux-gnu
     │ │   [24/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_acosd.for.o
     │ │   [25/134] Compiling C object sources/pytexture.cpython-313-x86_64-linux-gnu.so.p/pytexturemodule.c.o
     │ │   [26/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_cosd.for.o
     │ │   [27/134] Compiling C object sources/pack_f.cpython-313-x86_64-linux-gnu.so.p/pack_fmodule.c.o
     │ │   [28/134] Generating dynamic dependency information for target texturesubs_lib
     │ │   [29/134] Generating dynamic dependency information for target NISTlatsubs_lib
     │ │   [30/134] Generating dynamic dependency information for target pytexture.cpython-313-x86_64-linux-gnu
     │ │   [31/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_hfunc.for.o
     │ │   [32/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_expint.for.o
     │ │   [33/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_lorentz.for.o
     │ │   [34/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_CENTER.f.o
     │ │   [35/134] Generating dynamic dependency information for target unpack_cbf.cpython-313-x86_64-linux-gnu
     │ │   [36/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_epsvoigt.for.o
     │ │   [37/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_gauleg.for.o
     │ │   [38/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_gerfc.for.o
     │ │   [39/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_psvoigt.for.o
     │ │   [40/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_HEAD4.f.o
     │ │   [41/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_HEAD0.f.o
     │ │   [42/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_DETERM.f.o
     │ │   [43/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_DERIV.f.o
     │ │   [44/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_CKPT02.f.o
     │ │   [45/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_DOT.f.o
     │ │   [46/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_psvfcjo.for.o
     │ │   [47/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_HEAD3.f.o
     │ │   [48/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_INVERS.f.o
     │ │   [49/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_HEAD2.f.o
     │ │   [50/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_psvfcjexpo.for.o
     │ │   [51/134] Compiling C object sources/histogram2d.cpython-313-x86_64-linux-gnu.so.p/histogram2dmodule.c.o
     │ │   [52/134] Compiling C object sources/fmask.cpython-313-x86_64-linux-gnu.so.p/fmask.c.o
     │ │   [53/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_HEAD5.f.o
     │ │   [54/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_MULTIP.f.o
     │ │   [55/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_SET.f.o
     │ │   [56/134] Compiling Fortran object sources/libpowsubs_lib.a.p/powsubs_psvfcj.f90.o
     │ │   [57/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_RD021.f.o
     │ │   [58/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_QMATRI.f.o
     │ │   [59/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_SHORTV.f.o
     │ │   [60/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_RD061.f.o
     │ │   [61/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_HEAD6.f.o
     │ │   [62/134] Compiling Fortran object sources/libNISTlatsubs_lib.a.p/NISTlatsubs_SPCON2.f.o
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     │ │   [203/206] /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1/GSASII/inputs/GSASIImacros/residue-rb.mac
     │ │   [204/206] /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1/GSASII/inputs/GSASIImacros/torsion.mac
     │ │   [205/206] /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1/.mesonpy-m6jcm80n/sources/convcell
     │ │   [206/206] /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1/.mesonpy-m6jcm80n/sources/LATTIC
     │ │   Preparing metadata (pyproject.toml): finished with status 'done'
     │ │   Source in /home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1 has version 2.0.0, which satisfies requirement GSAS-II==2.0.0 fr
     │ │ om file:///home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1
     │ │   Removed GSAS-II==2.0.0 from file:///home/tcaswell/.cache/rattler/cache/git-v0/checkouts/c5aaabe581fe7dd5/e0910fc1 from build tracker '/tmp/pip-build-trac
     │ │ ker-hdmjkcbn'
     │ │ Created temporary directory: /tmp/pip-unpack-ez3f799h
     │ │ Building wheels for collected packages: GSAS-II
     │ │   Created temporary directory: /tmp/pip-wheel-yc3x9jsz
     │ │   Destination directory: /tmp/pip-wheel-yc3x9jsz
     │ │   Building wheel for GSAS-II (pyproject.toml): started
     │ │   Running command Building wheel for GSAS-II (pyproject.toml)
     │ │   Building wheel for GSAS-II (pyproject.toml): finished with status 'done'
     │ │   Created wheel for GSAS-II: filename=gsas_ii-2.0.0-cp313-cp313-linux_x86_64.whl size=2856629 sha256=43bda054ce292b676d05be9fdba4136188e3b0fc173228f6485cf2
     │ │ f19895d184
     │ │   Stored in directory: /tmp/pip-ephem-wheel-cache-4hskxckz/wheels/a9/e3/1e/f3b6886d637460f6954dd6b389da58229e8fd2ddefabad2559
     │ │ Successfully built GSAS-II
     │ │ Installing collected packages: GSAS-II
     │ │   changing mode of $PREFIX/bin/GSAS-II to 755
     │ │ Successfully installed GSAS-II-2.0.0
     │ │ Removed build tracker: '/tmp/pip-build-tracker-hdmjkcbn'
     │ │
     │ ╰─────────────────── (took 9 seconds)
     │
     │ ╭─ Packaging new files
     │ │ Copying done!
     │ │ Relinking "pack_f.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "pytexture.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "fmask.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "pydiffax.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "pyspg.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "histogram2d.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "convcell"
     │ │ Relinking "LATTIC"
     │ │ Relinking "kvec_general.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "unpack_cbf.cpython-313-x86_64-linux-gnu.so"
     │ │ Relinking "pypowder.cpython-313-x86_64-linux-gnu.so"
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/kvec_general.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  ├─ libm.so.6
     │ │  └─ libc.so.6
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/histogram2d.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  └─ libc.so.6
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/pydiffax.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  ├─ libm.so.6
     │ │  ├─ libc.so.6
     │ │  ├─ lib/libgfortran.so.5.0.0 (libgfortran5)
     │ │  └─ libmvec.so.1
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/fmask.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  ├─ libc.so.6
     │ │  └─ libm.so.6
     │ │
     │ │ [bin/LATTIC] links against:
     │ │  ├─ libm.so.6
     │ │  ├─ libc.so.6
     │ │  └─ lib/libgfortran.so.5.0.0 (libgfortran5)
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/pack_f.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  └─ libc.so.6
     │ │
     │ │ [bin/convcell] links against:
     │ │  ├─ lib/libgfortran.so.5.0.0 (libgfortran5)
     │ │  ├─ libc.so.6
     │ │  └─ libm.so.6
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/unpack_cbf.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  ├─ libc.so.6
     │ │  └─ lib/libgfortran.so.5.0.0 (libgfortran5)
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/pytexture.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  ├─ libm.so.6
     │ │  └─ libc.so.6
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/pypowder.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  ├─ lib/libgfortran.so.5.0.0 (libgfortran5)
     │ │  ├─ libc.so.6
     │ │  └─ libm.so.6
     │ │
     │ │ [lib/python3.13/site-packages/GSASII/pyspg.cpython-313-x86_64-linux-gnu.so] links against:
     │ │  ├─ libc.so.6
     │ │  ├─ lib/libgfortran.so.5.0.0 (libgfortran5)
     │ │  └─ libm.so.6
     │ │ Post-processing done!
     │ │ Writing test files
     │ │ Writing metadata for package
     │ │ Copying license files
     │ │ Copying recipe files
     │ │
     │ │ Files in package:
     │ │   ├─ bin/GSAS-II (498 B) [prefix:text]
     │ │   ├─ bin/LATTIC (82.38 KiB)
     │ │   ├─ bin/convcell (31.05 KiB)
     │ │   ├─ lib/python3.13/site-packages/ElementTable.py (205 B)
     │ │   ├─ lib/python3.13/site-packages/GSASII/Absorb.py (27.82 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/Bilbao/BCS_API.py (29.87 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/Bilbao/__pycache__/BCS_API.cpython-313.pyc (27.81 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/ElementTable.py (19.54 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/FormFactors.py (41.73 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/G2compare.py (36.34 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/G2shapes.py (64.55 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIElem.py (33.97 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIElemGUI.py (15.15 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIGUI.py (4.29 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIIntPDFtool.py (45.15 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIconstrGUI.py (201.91 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIctrlGUI.py (458.13 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIdata.py (146.13 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIdataGUI.py (476.50 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIddataGUI.py (73.24 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIexprGUI.py (41.83 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIfiles.py (111.46 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIfpaGUI.py (34.88 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIimage.py (87.25 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIimgGUI.py (226.94 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIindex.py (46.42 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIlattice.py (143.65 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIImapvars.py (91.17 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIImath.py (242.79 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIImiscGUI.py (60.22 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIImpsubs.py (11.32 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIobj.py (93.59 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIpath.py (98.73 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIphsGUI.py (671.68 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIphsGUI2.py (103.46 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIplot.py (379.92 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIpwd.py (259.23 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSASIIpwdGUI.py (502.70 KiB)
     │ │   ├─ lib/python3.13/site-packages/GSASII/GSAS…
- .github/workflows/ci.yaml:33: prefix-dev/setup-pixi pixi-version v0.74.0 -> v0.83.0
- .github/workflows/ci.yaml:54: prefix-dev/setup-pixi pixi-version v0.74.0 -> v0.83.0
- .github/workflows/docs.yml:38: prefix-dev/setup-pixi pixi-version v0.74.0 -> v0.83.0
Copilot AI balanced review requested due to automatic review settings October 23, 2026 15:29

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🟢 Approval recommended

The manifest requirements, lockfile updates, and workflow pins are consistent, with no blocking issues identified.

No open issues 🎉

What changed in this PR

This PR updates PowderLine’s dependency environment and CI tooling to address the emSign CA incident without changing application code.

Changes:

  • Requires Pixi ≥0.82.1 and pip ≥26.2.2.
  • Refreshes locked certificate packages and pip across both environments and all supported platforms.
  • Updates test and documentation workflows to Pixi v0.83.0.
File Description
pixi.toml Sets minimum patched Pixi and pip versions.
pixi.lock Updates certificate packages, pip, and associated lock metadata.
.github/​workflows/​docs.yml Uses Pixi v0.83.0 for documentation deployment.
.github/​workflows/​ci.yaml Uses Pixi v0.83.0 for tests and documentation validation.

Review effort: Balanced

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2 participants