From fc4a0df2f60c6e96a35d60afb2f4ea4e41884f8f Mon Sep 17 00:00:00 2001
From: Ted Kisner <tskisner.public@gmail.com>
Date: Thu, 23 Jan 2025 21:07:37 -0800
Subject: [PATCH 1/7] Include python-3.13 in test matrix.  Bump release
 version.

---
 .github/workflows/deploy.yml                  | 18 ++++++++++++++++--
 .github/workflows/test.yml                    |  8 ++++----
 .github/workflows/wheels.yml                  | 18 ++++++++++++++++--
 packaging/conda/install_deps_conda.sh         |  2 +-
 .../conda/install_deps_conda_external.sh      |  2 +-
 packaging/deps/cfitsio.sh                     |  2 +-
 packaging/wheels/install_deps_linux.sh        | 19 +------------------
 packaging/wheels/install_deps_osx.sh          | 19 +------------------
 src/toast/RELEASE                             |  2 +-
 9 files changed, 42 insertions(+), 48 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index abf46892e..9f104a137 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -42,6 +42,10 @@ jobs:
             arch: x86_64
             python: 312
             builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 313
+            builder: manylinux
 
           # MacOS x86_64.  The macos-13 runner is the last
           # Intel-based runner version.  At some point we'll
@@ -61,6 +65,11 @@ jobs:
             python: 312
             builder: macosx
             deploy: 13.0
+          - os: macos-13
+            arch: x86_64
+            python: 313
+            builder: macosx
+            deploy: 13.0
 
           # MacOS arm64
           - os: macos-latest
@@ -78,6 +87,11 @@ jobs:
             python: 312
             builder: macosx
             deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 313
+            builder: macosx
+            deploy: 14.0
     env:
       CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
       CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.builder }}2014
@@ -117,11 +131,11 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install twine cibuildwheel==2.20.0
+          python -m pip install twine cibuildwheel==2.22.0
 
       - name: Build wheel
         run: |
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8c005c1ea..401d4020f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -36,11 +36,11 @@ jobs:
             arch: Linux-x86_64
             ompdisable: 0
           - os: ubuntu-latest
-            python: "3.10"
+            python: "3.12"
             arch: Linux-x86_64
             ompdisable: 0
           - os: ubuntu-latest
-            python: "3.12"
+            python: "3.13"
             arch: Linux-x86_64
             ompdisable: 0
           - os: macos-latest
@@ -48,7 +48,7 @@ jobs:
             arch: MacOSX-x86_64
             ompdisable: 1
           - os: macos-latest
-            python: "3.12"
+            python: "3.13"
             arch: MacOSX-x86_64
             ompdisable: 1
           - os: macos-latest
@@ -56,7 +56,7 @@ jobs:
             arch: MacOSX-arm64
             ompdisable: 1
           - os: macos-latest
-            python: "3.12"
+            python: "3.13"
             arch: MacOSX-arm64
             ompdisable: 1
     steps:
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index 8ae8938bb..9db474f93 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -44,6 +44,10 @@ jobs:
             arch: x86_64
             python: 312
             builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 313
+            builder: manylinux
 
           # MacOS x86_64.  The macos-13 runner is the last
           # Intel-based runner version.  At some point we'll
@@ -63,6 +67,11 @@ jobs:
             python: 312
             builder: macosx
             deploy: 13.0
+          - os: macos-13
+            arch: x86_64
+            python: 313
+            builder: macosx
+            deploy: 13.0
 
           # MacOS arm64
           - os: macos-latest
@@ -80,6 +89,11 @@ jobs:
             python: 312
             builder: macosx
             deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 313
+            builder: macosx
+            deploy: 14.0
     env:
       CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
       CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.builder }}2014
@@ -128,11 +142,11 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==2.20.0
+          python -m pip install cibuildwheel==2.22.0
 
       - name: Build wheel
         run: |
diff --git a/packaging/conda/install_deps_conda.sh b/packaging/conda/install_deps_conda.sh
index f815bf6c8..805cb5182 100755
--- a/packaging/conda/install_deps_conda.sh
+++ b/packaging/conda/install_deps_conda.sh
@@ -7,7 +7,7 @@ envname=$1
 # Explicit python version to use
 pyversion=$2
 if [ "x${pyversion}" = "x" ]; then
-    pyversion=3.10
+    pyversion=3.12
 fi
 
 # Install optional dependencies if desired
diff --git a/packaging/conda/install_deps_conda_external.sh b/packaging/conda/install_deps_conda_external.sh
index 846b71276..843ed2929 100755
--- a/packaging/conda/install_deps_conda_external.sh
+++ b/packaging/conda/install_deps_conda_external.sh
@@ -7,7 +7,7 @@ envname=$1
 # Explicit python version to use
 pyversion=$2
 if [ "x${pyversion}" = "x" ]; then
-    pyversion=3.10
+    pyversion=3.12
 fi
 
 # Install optional dependencies if desired
diff --git a/packaging/deps/cfitsio.sh b/packaging/deps/cfitsio.sh
index f1617154f..b134790dc 100644
--- a/packaging/deps/cfitsio.sh
+++ b/packaging/deps/cfitsio.sh
@@ -7,7 +7,7 @@
 # - STATIC (yes/no)
 # - CLEANUP (yes/no)
 
-cfitsio_version=4.3.0
+cfitsio_version=4.5.0
 cfitsio_dir=cfitsio-${cfitsio_version}
 cfitsio_pkg=${cfitsio_dir}.tar.gz
 
diff --git a/packaging/wheels/install_deps_linux.sh b/packaging/wheels/install_deps_linux.sh
index b73d56b2a..c74e4e128 100755
--- a/packaging/wheels/install_deps_linux.sh
+++ b/packaging/wheels/install_deps_linux.sh
@@ -69,27 +69,10 @@ pip install --upgrade pip
 # Install a couple of base packages that are always required
 pip install -v cmake wheel
 
-# In order to maximize ABI compatibility with numpy, build with the newest numpy
-# version containing the oldest ABI version compatible with the python we are using.
-# NOTE: for now, we build with numpy 2.0.x, which is backwards compatible with
-# numpy-1.x and forward compatible with numpy-2.x.
 pyver=$(python3 --version 2>&1 | awk '{print $2}' | sed -e "s#\(.*\)\.\(.*\)\..*#\1.\2#")
-# if [ ${pyver} == "3.8" ]; then
-#     numpy_ver="1.20"
-# fi
-# if [ ${pyver} == "3.9" ]; then
-#     numpy_ver="1.20"
-# fi
-# if [ ${pyver} == "3.10" ]; then
-#     numpy_ver="1.22"
-# fi
-# if [ ${pyver} == "3.11" ]; then
-#     numpy_ver="1.24"
-# fi
-numpy_ver="2.0.1"
 
 # Install build requirements.
-CC="${CC}" CFLAGS="${CFLAGS}" pip install -v -r "${scriptdir}/build_requirements.txt" "numpy==${numpy_ver}"
+CC="${CC}" CFLAGS="${CFLAGS}" pip install -v -r "${scriptdir}/build_requirements.txt" numpy
 
 # Build compiled dependencies
 
diff --git a/packaging/wheels/install_deps_osx.sh b/packaging/wheels/install_deps_osx.sh
index ca85cd595..dc74b945b 100755
--- a/packaging/wheels/install_deps_osx.sh
+++ b/packaging/wheels/install_deps_osx.sh
@@ -77,27 +77,10 @@ pip install --upgrade pip
 # Install a couple of base packages that are always required
 pip install -v wheel
 
-# In order to maximize ABI compatibility with numpy, build with the newest numpy
-# version containing the oldest ABI version compatible with the python we are using.
-# NOTE: for now, we build with numpy 2.0.x, which is backwards compatible with
-# numpy-1.x and forward compatible with numpy-2.x.
 pyver=$(python3 --version 2>&1 | awk '{print $2}' | sed -e "s#\(.*\)\.\(.*\)\..*#\1.\2#")
-# if [ ${pyver} == "3.8" ]; then
-#     numpy_ver="1.20"
-# fi
-# if [ ${pyver} == "3.9" ]; then
-#     numpy_ver="1.24"
-# fi
-# if [ ${pyver} == "3.10" ]; then
-#     numpy_ver="1.24"
-# fi
-# if [ ${pyver} == "3.11" ]; then
-#     numpy_ver="1.24"
-# fi
-numpy_ver="2.0.1"
 
 # Install build requirements.
-CC="${CC}" CFLAGS="${CFLAGS}" pip install -v -r "${scriptdir}/build_requirements.txt" "numpy==${numpy_ver}"
+CC="${CC}" CFLAGS="${CFLAGS}" pip install -v -r "${scriptdir}/build_requirements.txt" numpy
 
 # Build compiled dependencies
 
diff --git a/src/toast/RELEASE b/src/toast/RELEASE
index fb0455491..816e4a092 100644
--- a/src/toast/RELEASE
+++ b/src/toast/RELEASE
@@ -1 +1 @@
-3.0.0a28
+3.0.0a29

From 61be4b5ce3fa77fd9d092843f0829645ba6e2f5f Mon Sep 17 00:00:00 2001
From: Ted Kisner <tskisner.public@gmail.com>
Date: Thu, 23 Jan 2025 21:28:27 -0800
Subject: [PATCH 2/7] conda-build is no longer needed

---
 packaging/conda/install_deps_conda.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packaging/conda/install_deps_conda.sh b/packaging/conda/install_deps_conda.sh
index 805cb5182..2c29121e5 100755
--- a/packaging/conda/install_deps_conda.sh
+++ b/packaging/conda/install_deps_conda.sh
@@ -62,7 +62,7 @@ for pfile in ${pkgfiles}; do
     plist=$(cat "${pfile}" | xargs -I % echo -n '"%" ')
     pkglist="${pkglist} ${plist}"
 done
-pkglist="python=${pyversion} ${pkglist} compilers conda-build"
+pkglist="python=${pyversion} ${pkglist} compilers"
 echo "Installing conda packages:  ${pkglist}"
 conda install --yes --update-all ${pkglist}
 # The "cc" symlink breaks Crays...

From 3410c3f06984b2aa2c69e43498938214cb17c8b3 Mon Sep 17 00:00:00 2001
From: Ted Kisner <tskisner.public@gmail.com>
Date: Thu, 23 Jan 2025 22:42:25 -0800
Subject: [PATCH 3/7] Check wheel tests.

---
 .github/workflows/test.yml   |  8 ++++----
 .github/workflows/wheels.yml | 23 ++++++++++++-----------
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 401d4020f..683302275 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -11,10 +11,10 @@ on:
   push:
     branches:
       - master
-  pull_request:
-    branches:
-      - master
-      - toast3
+  # pull_request:
+  #   branches:
+  #     - master
+  #     - toast3
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index 9db474f93..be8f80f55 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -1,17 +1,18 @@
 
 name:  Test Binary Wheels
 
-on: workflow_dispatch
-# FIXME:  Remove these lines once this workflow merged
-# to main branch.
-# on:
-#   push:
-#     branches:
-#       - master
-#   pull_request:
-#     branches:
-#       - master
-#       - toast3
+
+on:
+  workflow_dispatch:
+  # FIXME:  Remove these lines once this workflow merged
+  # to main branch.
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+      - toast3
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

From 34e5dfed0da6ea06579104fb9140d350f798c4f8 Mon Sep 17 00:00:00 2001
From: Ted Kisner <tskisner.public@gmail.com>
Date: Thu, 23 Jan 2025 23:18:59 -0800
Subject: [PATCH 4/7] Use tomlkit instead of toml, to avoid bringing in a new,
 trivial dependency.

---
 src/toast/ops/sim_catalog.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/toast/ops/sim_catalog.py b/src/toast/ops/sim_catalog.py
index 45216ec39..6734b2e4a 100644
--- a/src/toast/ops/sim_catalog.py
+++ b/src/toast/ops/sim_catalog.py
@@ -7,7 +7,7 @@
 import h5py
 import healpy as hp
 import numpy as np
-import toml
+import tomlkit
 import traitlets
 from astropy.stats import gaussian_fwhm_to_sigma
 from astropy import units as u
@@ -194,7 +194,7 @@ def _load_catalog(self):
         log = Logger.get()
         # Load the TOML into a dictionary
         with open(self.catalog_file, "r") as f:
-            self.catalog = toml.loads(f.read())
+            self.catalog = tomlkit.parse(f.read())
         # Check that the necessary keys are defined for every source
         for source_name, source_dict in self.catalog.items():
             for key in ["ra_deg", "dec_deg", "freqs_ghz"]:

From 171a57b4309cb9e804254b09286f91eed507e37f Mon Sep 17 00:00:00 2001
From: Ted Kisner <tskisner.public@gmail.com>
Date: Thu, 23 Jan 2025 23:57:39 -0800
Subject: [PATCH 5/7] Another place where toml was used instead of tomlkit

---
 src/toast/tests/ops_sim_tod_catalog.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/toast/tests/ops_sim_tod_catalog.py b/src/toast/tests/ops_sim_tod_catalog.py
index 8d538073e..949413c2d 100644
--- a/src/toast/tests/ops_sim_tod_catalog.py
+++ b/src/toast/tests/ops_sim_tod_catalog.py
@@ -4,7 +4,7 @@
 
 import os
 
-import toml
+import tomlkit
 import healpy as hp
 import numpy as np
 from astropy import units as u
@@ -78,7 +78,7 @@ def setUp(self):
             }
 
             with open(self.catalog_file, "w") as f:
-                f.write(toml.dumps(catalog))
+                f.write(tomlkit.dumps(catalog))
 
         if self.comm is not None:
             self.comm.barrier()

From 16f9b7d1c35b7f00e860e4bbfee1497e868502b1 Mon Sep 17 00:00:00 2001
From: Ted Kisner <tskisner.public@gmail.com>
Date: Fri, 24 Jan 2025 00:54:03 -0800
Subject: [PATCH 6/7] Arrays are not compatible with toml table

---
 src/toast/ops/sim_catalog.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/toast/ops/sim_catalog.py b/src/toast/ops/sim_catalog.py
index 6734b2e4a..b272d20cb 100644
--- a/src/toast/ops/sim_catalog.py
+++ b/src/toast/ops/sim_catalog.py
@@ -233,7 +233,7 @@ def _load_catalog(self):
         for source_name, source_dict in self.catalog.items():
             lon = source_dict["ra_deg"]
             lat = source_dict["dec_deg"]
-            source_dict["vec"] = hp.dir2vec(lon, lat, lonlat=True)
+            source_dict["vec"] = hp.dir2vec(lon, lat, lonlat=True).tolist()
         return
 
     def __init__(self, **kwargs):

From 748efbbfe6231671be0ff21acee0f53361134d7d Mon Sep 17 00:00:00 2001
From: Ted Kisner <tskisner.public@gmail.com>
Date: Fri, 24 Jan 2025 07:48:55 -0800
Subject: [PATCH 7/7] Restore normal testing

---
 .github/workflows/test.yml   |  8 ++++----
 .github/workflows/wheels.yml | 15 +++++++--------
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 683302275..401d4020f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -11,10 +11,10 @@ on:
   push:
     branches:
       - master
-  # pull_request:
-  #   branches:
-  #     - master
-  #     - toast3
+  pull_request:
+    branches:
+      - master
+      - toast3
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index be8f80f55..f95696801 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -1,18 +1,17 @@
 
 name:  Test Binary Wheels
 
-
 on:
   workflow_dispatch:
   # FIXME:  Remove these lines once this workflow merged
   # to main branch.
-  push:
-    branches:
-      - master
-  pull_request:
-    branches:
-      - master
-      - toast3
+  # push:
+  #   branches:
+  #     - master
+  # pull_request:
+  #   branches:
+  #     - master
+  #     - toast3
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}