Release v?? -- Glacier summer school

.github/workflows/build.yml

@@ -14,7 +14,7 @@ on:
 jobs:
   call-version-info-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.21.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.21.1
     permissions:
       contents: read
     with:
@@ -23,7 +23,7 @@ jobs:
   call-docker-ghcr-workflow:
     needs: call-version-info-workflow
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.21.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.21.1
     permissions:
       contents: read
       packages: write

.github/workflows/changelog.yml

@@ -14,6 +14,6 @@ on:
 jobs:
   call-changelog-check-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.21.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.21.1
     permissions:
       contents: read

.github/workflows/labeled-pr.yml

@@ -13,6 +13,6 @@ on:
 jobs:
   call-labeled-pr-check-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.21.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.21.1
     permissions:
       pull-requests: read

.github/workflows/release.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   call-release-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.21.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.21.1
     permissions: {}
     with:
       release_prefix: pism-terra

.github/workflows/static-analysis.yml

@@ -5,7 +5,7 @@ on: push
 jobs:
   call-secrets-analysis-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.21.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.21.1
     permissions:
       contents: read
 
@@ -23,7 +23,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: environment.yml
           create-args: >-
@@ -33,4 +33,4 @@ jobs:
       - name: run pylint
         shell: bash -el {0}
         run: |
-          pylint -v --extension-pkg-whitelist=scipy $(git ls-files '*.py')
+          pylint -v --extension-pkg-whitelist=scipy,rasterio $(git ls-files '*.py')

.github/workflows/tag-version.yml

@@ -9,7 +9,7 @@ jobs:
   call-bump-version-workflow:
     # For first-time setup, create a v0.0.0 tag as shown here:
     # https://github.com/ASFHyP3/actions#reusable-bump-versionyml
-    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.21.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.21.1
     permissions: {}
     with:
       user: jhkennedy

.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: environment.yml
           create-args: >-

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: "docs|node_modules|migrations|.git|.tox"
+exclude: "docs/_build|docs/source/auto_examples|docs/source/reference/generated|node_modules|migrations|.git|.tox"
 default_stages: [pre-commit]
 fail_fast: true
 
@@ -8,18 +8,19 @@ repos:
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
+      - id: check-toml
       - id: check-yaml
         exclude: conda/meta.yaml
 
   # Can run individually with `pre-commit run black --all-files`
   - repo: https://github.com/psf/black
-    rev: 26.3.1
+    rev: 26.5.1
     hooks:
       - id: black
 
   # Can run individually with `pre-commit run isort --all-files`
   - repo: https://github.com/timothycrosley/isort
-    rev: 8.0.1
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args:
@@ -32,16 +33,23 @@ repos:
     rev: v1.10.0
     hooks:
       - id: numpydoc-validation
+        exclude: ^(pism_terra/kitp/writer\.py|docs/source/conf\.py)$
 
   # Can run individually with `pre-commit run mypy --all-files`
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v2.1.0
     hooks:
       - id: mypy
         args: ["--config-file", "pyproject.toml", "--ignore-missing-imports"]
+        exclude: ^pism_terra/kitp/writer\.py$
         additional_dependencies: [types-toml, types-requests]
 
 
+  - repo: https://github.com/srstevenson/nb-clean
+    rev: 4.0.1
+    hooks:
+     - id: nb-clean
+
   - repo: local
     hooks:
       - id: pylint
@@ -50,25 +58,23 @@ repos:
         language: system
         types: [python]
         require_serial: true
+        exclude: ^pism_terra/kitp/writer\.py$
         args:
           [
             "-rn", # Only display messages
             "-sn", # Don't display the score
             "--extension-pkg-whitelist=scipy",
           ]
 
-  - repo: https://github.com/srstevenson/nb-clean
-    rev: 4.0.1
-    hooks:
-     - id: nb-clean
 
-  # - repo: local
-  #   hooks:
-  #   - id: pytest # pytest is a pre-commit hook
-  #     name: pytest
-  #     entry: pytest tests
-  #     language: system
-  #     types: [python]
-  #     exclude: ^venv/ ^.git/ ^.vscode/ ^.DS_Store ^uq/ ^hindcasts/
-  #     always_run: true
-  #     pass_filenames: false
+  - repo: local
+    hooks:
+    - id: pytest
+      name: pytest
+      entry: pytest tests
+      language: system
+      types: [python]
+      exclude: ^venv/ ^.git/ ^.vscode/ ^.DS_Store ^uq/ ^hindcasts/
+      always_run: true
+      pass_filenames: false
+      stages: [pre-push]

.readthedocs.yaml

@@ -0,0 +1,23 @@
+# Read the Docs configuration for pism-terra.
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.13"
+
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+formats:
+  - htmlzip

CHANGELOG.md

@@ -8,9 +8,28 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+### Changed
+- `glacier.execute` no longer accepts a `--job-id` parameter and now stages files based on the full S3 URI of `RUN_SCIPT`, if needed.
+
 ### Fixed
 
 - missing force_to_thickness.file
+- runtime environment is now default, for dev work use environment-dev.yml.
+- merged missing commits from summer school
+- updated Docker image to pull to fix build bug in pism/pism
+- improved postprocessing of RGI
+- fixed missing output filename for inverse state
+- fixed missing resolve()
+- fixed initialization
+- fixed CLI for stress balance
+- fixed SNAP climate
+- fixed environment-dev.yml
+
+### Added
+
+- compliance checker run after simulation
+- notebooks/pism_cloud_app.ipynb, a `voila` app.
+- pism_terra/glacier/render_terrain_3.py
 
 ## [0.1.3]
 

CITATION.cff

@@ -0,0 +1,73 @@
+# -*- mode: yaml -*-
+#
+# Run
+#
+# git shortlog -sn --no-merges `branch`
+#
+# to list contributors to a `branch` and the number of non-merge commits they made.
+#
+# Output as of 2026-05-01 (branch=dev)
+#
+#   244  Andy Aschwanden
+#    50  Joseph H Kennedy
+#     1  Bruno Belotti
+#     1  dependabot[bot]
+#
+# Total: 7
+#
+# Overall total: 32
+#
+# To validate this document, install `cffconvert`
+#
+# python3 -m pip install cffconvert --user
+#
+# and run
+#
+# cffconvert --validate
+#
+# Note: the CITATION.cff format does not allow for extra information, so
+# "contribution-areas" below are commented out. These lines *are* needed to generate the
+# list of authors in the manual, though. Each author should have a list of contribution
+# areas *one one line*, indented so that the substitution "s/# contrib/contrib/g" will
+# produce a valid YAML document.
+#
+# See doc/sphinx/Makefile and doc/sphinx/authorship.py for details.
+
+cff-version: 1.2.0
+title: 'PISM Terra'
+type: software
+doi: 10.5281/zenodo.1199019
+contact:
+  - email: uaf-pism@alaska.edu
+    name: "PISM developers at UAF"
+authors:
+  - given-names: Andy
+    family-names: Aschwanden
+    email: aaschwanden@alaska.edu
+    affiliation: University of Alaska Fairbanks
+    orcid: 'https://orcid.org/0000-0001-8149-2315'
+  - given-names: Joseph H
+    family-names: Kennedy
+    email: jhkennedy@alaska.edu
+    affiliation: University of Alaska Fairbanks
+    orcid: https://orcid.org/0000-0002-9348-693X'
+
+repository-code: 'https://github.com/pism/pism-terra'
+url: 'https://www.pism.io'
+
+abstract: The Parallel Ice Sheet Model (PISM) is an open-source modelling framework for
+  ice sheets and glaciers. Its features include a hierarchy of available stress balances,
+  marine ice sheet physics with dynamic calving fronts, an enthalpy-based conservation of
+  energy scheme, bed deformation and subglacial hydrology components, extensible coupling
+  to atmospheric and ocean models, and comprehensive user documentation. PISM uses
+  distributed-memory (PETSc- and MPI-based) parallelism for high-resolution simulations.
+
+  PISM is jointly developed at the University of Alaska, Fairbanks (UAF) and the Potsdam
+  Institute for Climate Impact Research (PIK).
+
+keywords:
+  - ice sheet model
+  - open source
+  - geophysics
+  - sea level
+license: GPL-3.0-or-later

CLAUDE.md

@@ -17,6 +17,43 @@ conda activate pism-terra
 python -m pip install -e .
 ```
 
+### Required environment workaround: `LD_PRELOAD` libz
+
+On affected conda-forge envs, `liborc.so` (a transitive dep of `pyarrow`) re-exports
+zlib's full deflate API as global symbols. When libgdal calls `deflateInit_` during
+GeoTIFF compression — including the in-memory `MemoryFile` writes that
+`dem_stitcher` uses to mosaic DEM tiles — the dynamic loader binds it to liborc's
+internal copy instead of `libz.so.1`. The two implementations have incompatible
+heap layouts, so any subsequent realloc/free on that buffer corrupts the heap
+and the next unrelated `_int_malloc` aborts with:
+
+```
+Fatal glibc error: malloc.c:4241 (_int_malloc): assertion failed:
+    (unsigned long) (size) >= (unsigned long) (nb)
+```
+
+Workaround: preload conda's libz so it wins symbol resolution. The repo's
+`environment.yml` does **not** wire this up automatically — you need it in your
+shell, ideally as an env activation hook:
+
+```bash
+mkdir -p $CONDA_PREFIX/etc/conda/activate.d $CONDA_PREFIX/etc/conda/deactivate.d
+cat > $CONDA_PREFIX/etc/conda/activate.d/zz-libz-preload.sh <<'EOF'
+export _PISM_TERRA_OLD_LD_PRELOAD="$LD_PRELOAD"
+export LD_PRELOAD="$CONDA_PREFIX/lib/libz.so.1${LD_PRELOAD:+:$LD_PRELOAD}"
+EOF
+cat > $CONDA_PREFIX/etc/conda/deactivate.d/zz-libz-preload.sh <<'EOF'
+export LD_PRELOAD="$_PISM_TERRA_OLD_LD_PRELOAD"
+unset _PISM_TERRA_OLD_LD_PRELOAD
+EOF
+```
+
+Verify: `nm -D --defined-only $CONDA_PREFIX/lib/liborc.so | grep -c "T deflate"`.
+A non-zero result means the leak is still present and `LD_PRELOAD` is required.
+Once it returns `0` (after a future liborc rebuild), the preload can be removed.
+
+Tracking: see https://github.com/conda-forge/orc-feedstock/issues for upstream.
+
 ## Commands
 
 ### Running Tests

Dockerfile

@@ -1,4 +1,5 @@
-ARG PISM_TAG=2.3.0
+ # This is the merge of the feature/inverse branch to dev
+ARG PISM_TAG=dev
 FROM ghcr.io/pism/pism:${PISM_TAG} AS runtime
 
 FROM runtime AS build