From 6a95128082c0d5a944dff0cccb174a312bf32948 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Sun, 20 Aug 2023 18:18:03 -0700
Subject: [PATCH 01/13] Bump pixell version, WIP on modulefiles

---
 pkgs/pixell/meta.yaml       |  4 ++--
 templates/modulefile_lua.in | 19 ++++++++++++++++++-
 templates/modulefile_tcl.in |  8 ++++++--
 3 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/pkgs/pixell/meta.yaml b/pkgs/pixell/meta.yaml
index 5a8d30a..7d36fe6 100644
--- a/pkgs/pixell/meta.yaml
+++ b/pkgs/pixell/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.17.3" %}
-{% set sha256 = "335742bb22a535add21dd6e63eb9bf35ee98c97efd2795989ca449d1fdc38ad1" %}
+{% set version = "0.19.0" %}
+{% set sha256 = "8142a2a368175de845166afffe3e4efd0ac0bdc109a96eb8f4cc0360e6191fd1" %}
 
 {% set build = 0 %}
 
diff --git a/templates/modulefile_lua.in b/templates/modulefile_lua.in
index 23c3b87..3b4ccdc 100644
--- a/templates/modulefile_lua.in
+++ b/templates/modulefile_lua.in
@@ -15,7 +15,7 @@ whatis("Version: " .. "@VERSION@")
 whatis("URL: " .. "https://github.com/simonsobs/soconda")
 whatis("Description: " .. "Simons Observatory Conda Tools")
 
-conflict("sohpc", "so-env", "soconda")
+conflict("sohpc", "so-env", "soconda", "python")
 
 -- Dependency module commands
 @MODLOAD@
@@ -36,6 +36,23 @@ setenv("CONDA_SHLVL", "1")
 setenv("CONDA_DEFAULT_ENV", "@ENVPREFIX@")
 prepend_path("PATH", "@ENVPREFIX@/bin")
 
+local funcs = "conda __conda_activate __conda_hashr __conda_reactivate __add_sys_prefix_to_path"
+
+execute{cmd="source " .. @BASE@ .. "/etc/profile.d/conda.sh; conda activate @ENVNAME@; export -f " .. funcs, modeA={"load"}}
+
+execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; pre=" .. conda_dir .. "; \
+	export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
+	export PATH=$(echo ${PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
+        unset -f " .. funcs .. "; \
+    unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\" | /bin/grep -v 'CONDA_ENVS_PATH\\|CONDA_PKGS_DIRS');", modeA={"unload"}}
+
+execute{cmd="source " .. conda_dir .. "/etc/profile.d/conda.sh; conda activate py${PYV}_${ENV}; export -f " .. funcs, modeA={"load"}}
+execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; pre=" .. conda_dir .. "; \
+	export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
+	export PATH=$(echo ${PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
+        unset -f " .. funcs .. "; \
+
+
 -- Create a versioned user directory for local pip installation
 local userbase = pathJoin(HOME, ".local", "soconda", "@VERSION@")
 setenv("PYTHONUSERBASE", userbase)
diff --git a/templates/modulefile_tcl.in b/templates/modulefile_tcl.in
index 85f89a2..e4e1f96 100644
--- a/templates/modulefile_tcl.in
+++ b/templates/modulefile_tcl.in
@@ -14,11 +14,15 @@ proc ModulesHelp { } {
     puts stderr ""
 }
 
-conflict sohpc so-env soconda
+conflict sohpc so-env soconda python
 
 # Dependency module commands
 @MODLOAD@
 
+if {[module-info command unload]} {
+    system AUTO_ACTIVATE_BASE=false @BASE@/bin/conda deactivate
+}
+
 # This might be set by OS python and gives us problems.
 unsetenv PYTHONSTARTUP
 
@@ -27,7 +31,7 @@ unsetenv PYTHONSTARTUP
 # calls do not work.  This solution could be fragile, so should
 # be revisited in the future.
 
-setenv CONDA_EXE "@BASE@/bin/conda"
+setenv CONDA_EXE @BASE@/bin/conda
 setenv CONDA_PYTHON_EXE "@BASE@/bin/python"
 setenv CONDA_PREFIX "@ENVPREFIX@"
 setenv CONDA_PROMPT_MODIFIER ""

From c1c8c1dad010102d30cb8437b62c0f7dda593de1 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Tue, 22 Aug 2023 14:18:55 -0700
Subject: [PATCH 02/13] Work on docs

---
 docs/docs/automate.md |   1 +
 docs/docs/dev.md      |  57 +++++++++++++++++
 docs/docs/index.md    |  14 ++++
 docs/docs/install.md  | 146 ++++++++++++++++++++++++++++++++++++++++++
 docs/docs/usage.md    |  41 ++++++++++++
 docs/mkdocs.yml       |  15 +++++
 6 files changed, 274 insertions(+)
 create mode 100644 docs/docs/automate.md
 create mode 100644 docs/docs/dev.md
 create mode 100644 docs/docs/index.md
 create mode 100644 docs/docs/install.md
 create mode 100644 docs/docs/usage.md
 create mode 100644 docs/mkdocs.yml

diff --git a/docs/docs/automate.md b/docs/docs/automate.md
new file mode 100644
index 0000000..6f36009
--- /dev/null
+++ b/docs/docs/automate.md
@@ -0,0 +1 @@
+# Automating the Install
diff --git a/docs/docs/dev.md b/docs/docs/dev.md
new file mode 100644
index 0000000..cafde5d
--- /dev/null
+++ b/docs/docs/dev.md
@@ -0,0 +1,57 @@
+# Developer Notes
+
+This section covers steps needed when maintaining the `soconda` tools.
+
+## Releases
+
+After updating the versions of included packages, it is a good idea to make a
+new release so that a new environment is built and deployed. After all
+outstanding changes are merged to `main`, go to the github page for this
+repository and click on the `Actions` tab. Trigger the `Test Build` workflow.
+This will take an hour or so to run. Assuming it all works, create a new
+release with some notes about what was updated. Cron jobs running on our
+computing centers will check for new tags and build them if found.
+
+## Changing Installed Packages
+
+The three top-level files: `packages_conda.txt`, `packages_local.txt`, and
+`packages_pip.txt` contain the packages that will be installed. The conda
+packages are installed first, then local conda packages are built and
+installed, and finally the pip packages are installed. When installing pip
+packages, the `soconda.sh` script first extracts the dependencies of each pip
+package and installs it instead with conda. This helps minimize the number of
+pip packages installed in the environment and that makes it easier to avoid
+dependency problems later.
+
+## Updating Bundled Recipes
+
+The conda recipes for bundled packages should be updated whenever upstream
+packages have new releases. This involves the following steps:
+
+1.  Update the version in the `meta.yaml` file of the package recipe.
+
+2.  Update the download URL if needed.
+
+3.  Manually download the new tarball of the package.  For example:
+
+        curl -SL -o pixel-0.19.0.tar.gz \
+        https://github.com/simonsobs/pixell/archive/v0.19.0.tar.gz
+
+4. Get the sha256 checksum of the tarball, and copy that into the `meta.yaml`
+entry:
+
+        openssl sha256 pixel-0.19.0.tar.gz
+        SHA256(pixell-0.19.0.tar.gz)= 8142a2a368175de845166afffe3e4efd0ac0bdc109a96eb8f4cc0360e6191fd1
+
+5. Ensure that the new version of the package does not have any updated
+dependencies or other constraints.
+
+## Adding New Package Recipes
+
+This should not be needed very often, and will require some familiarity with
+conda recipes. Create a new directory for the recipe in the `pkgs` directory.
+Add a `meta.yaml` file, a `build.sh` file, and a copy of the package license.
+See the conda documentation and existing conda-forge feedstocks for extensive
+examples. You can load an existing soconda environment as a testbed and then
+test your new recipe with `conda build`. After you can build it independently,
+add it to the `packages_local.txt` file.
diff --git a/docs/docs/index.md b/docs/docs/index.md
new file mode 100644
index 0000000..c757ece
--- /dev/null
+++ b/docs/docs/index.md
@@ -0,0 +1,14 @@
+# Simons Observatory Conda Tools
+
+This repository contains scripts to help with:
+
+- Installing a conda base system (optional)
+
+- Creating a conda environment with a well-defined set of conda and pip packages
+
+- Building a few legacy compiled packages into this environment
+
+- Creating a versioned modulefile for loading the environment
+
+The documentation also covers different user scenarios for loading and
+customizing a pre-installed environment.
diff --git a/docs/docs/install.md b/docs/docs/install.md
new file mode 100644
index 0000000..9ebb66a
--- /dev/null
+++ b/docs/docs/install.md
@@ -0,0 +1,146 @@
+# Creating a Simons Observatory Environment
+
+The install script takes options to specify the location of the base environment
+(if it is not already activated) and the name (or full path) of the environment
+to create. It also allows specifying a central location to install the
+modulefile:
+
+    $> ./soconda.sh -h
+        Usage:  ./soconda.sh
+        [-e <environment, either name or full path>]
+        [-b <conda base install (if not activated)>]
+        [-v <version (git version used by default)>]
+        [-m <modulefile dir (default is <env>/modulefiles)>]
+        [-i <file with modulefile commands to load dependencies> ]
+
+---
+**NOTE**
+
+Running the `soconda.sh` script will create log files in the current directory.
+Consider running the command from within a temporary build directory to avoid
+clutter.
+
+---
+
+## Base Conda Environment
+
+If you already have a conda-forge base environment, then you can skip this
+step. Otherwise, decide on the install prefix for your overall conda
+environment. For this example, we will use `/opt/conda` as the path to the
+conda base installation. Now run the bootstrap script:
+
+    $> ./tools/bootstrap_base "/opt/conda"
+
+This bootstrap will install a base system with the conda-forge channel set to
+the default. You can now source the conda initialization file and activate the
+base environment:
+
+    $> source /opt/conda/etc/profile.d/conda.sh
+    $> conda activate base
+
+After installing an `soconda` environment below, you will not need this step
+since it is done by the generated modulefile.
+
+## Special Note on mpi4py
+
+By default, the conda package for mpi4py will be installed. This should work
+well for stand-alone workstations or single nodes. If you have a cluster with a
+customized MPI compiler, then set the `MPICC` environment variable to the MPI C
+compiler before creating an environment. That will cause the mpi4py package to
+be built using your compiler.
+
+## Example:  Local System
+
+Starting from scratch, bootstrap a small conda-forge base environment in `~/conda`:
+
+    $> ./tools/bootstrap_base.sh ~/conda
+    $> source ~/conda/etc/profile.d/conda.sh
+    $> conda activate base
+
+Create an `soconda` environment with default name and version. However, we
+decide to put all the modulefiles into a central location in the root of the
+base conda install:
+
+    $> ./soconda.sh -b ~/conda -m ~/conda/modulefiles
+
+Now we can load the module:
+
+    $> module use ~/conda/modulefiles
+    $> module avail
+    $> module load soconda/XXXXXX
+
+## Example:  NERSC
+
+At NERSC, the default provided python is from Anaconda, and does not work for
+our needs. Instead, we have a conda-forge base system installed in our project
+software directory:
+
+    $> source /global/common/software/sobs/perlmutter/conda/etc/profile.d/conda.sh
+    $> conda activate base
+
+Now we can either install a shared software environment or use this base environment to build a conda environment in a personal directory.  If you are installing to a shared software environment, you should do that as the project account and follow a specific naming convention which is beyond the scope of this document.  If you wanted to install these tools to your home directory you could do:
+
+    $> ./soconda.sh -b ~/conda_envs -m ~/conda_envs/modulefiles
+
+And then load the module:
+
+    $> module use ~/conda_envs/modulefiles
+    $> module avail
+    $> module load soconda/XXXXXX
+
+## Running Tests
+
+After loading an `soconda` environment, you can run some tests with:
+
+    $> ./run_tests.sh
+
+## Installing a Jupyter Kernel
+
+After loading an soconda module the first time, you can run (once) the included script:
+
+    $> soconda_jupyter.sh
+
+This will install a kernel file so that jupyter knows how to launch a kernel
+using this python stack.
+
+## Customizing an Environment
+
+If you want to dramatically change the package versions / content of an
+`soconda` stack, just load the existing base conda environment and edit the
+three lists of packages (`packages_[conda|pip|local].txt`) to exclude certain
+packages or add extras. Then install it as usual.
+
+## Deleting an Environment
+
+The `soconda` environments are self contained and you can delete them by
+removing the path or (if using a name), removing the `<base dir>/envs/<name of
+env>` directory. You can optionally delete the modulefile and the pip local
+directory in your home directory.
+
+## Advanced Details
+
+The compiled packages assume the use of the conda compilers for consistency with
+the libraries installed through conda. If you want to change those compilers you
+can remove the `compilers` conda package and manually set the `CC`, `CXX`, and `FC`
+environment variables. Full warning that this may cause problems with threading
+interfaces, thread pinning, etc, when building packages that use OpenMP.
+
+### Pixell
+
+We currently build pixell from source with the conda compilers for consistency,
+rather than installing the wheel.
+
+### So3g
+
+This package is currently installed from the wheel, but the conda package is
+being tested (using boost from conda-forge).
+
+### TOAST
+
+This package is currently built from source by default, with dependencies
+installed through conda. When toast-3.0 arrives in the conda-forge toast
+feedstock, it should be added back to `packages_conda.txt`. It should also work
+to install the python wheel package by commenting out the toast entry in
+`packages_local.txt` and adding it to `packages_pip.txt`.
+
+
diff --git a/docs/docs/usage.md b/docs/docs/usage.md
new file mode 100644
index 0000000..df6caa2
--- /dev/null
+++ b/docs/docs/usage.md
@@ -0,0 +1,41 @@
+# Using an Existing Environment
+
+If you are just using an already-created environment, you can follow
+instructions on the Simons Observatory project confluence site (see the Data
+Management pages on Computing Infrastructure) about where to find the
+installation for a particular system. After loading an environment, there are a
+several ways to customize things.
+
+## Overriding a Few Packages
+
+Each `soconda` modulefile sets the user directory (for `pip install --user`) to
+be in a versioned location in your home directory. If you want to use a
+different / newer version of `sotodlib` (for example), then you can just do:
+
+    $> pip install --user https://github.com/simonsobs/sotodlib/archive/master.tar.gz
+
+If you swap to a different `soconda` environment, your user package install
+directory will also switch.
+
+## More Extensive Customization
+
+One benefit of an `soconda` environment is that it also contains conda packages
+built for some legacy compiled tools. If you want to keep those, but
+dramatically change which other conda packages are installed, you can first
+create a new personal environment while cloning an existing one:
+
+    $> conda create --clone soconda_20230809_1.0.0 /path/to/my/env
+
+Then activate your new environment and conda install whatever you like:
+
+    $> conda activate /path/to/my/env
+    $> conda install foo bar blat
+
+Note that your pip user directory will still be set to the location created by
+the original upstream module, and you can also "`pip install --user`"
+additional packages to go with your custom conda environment.
+
+## Something Else
+
+You can also just load a conda base environment on a particular system and then
+read the next section of this document to install your own environment.
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
new file mode 100644
index 0000000..124d6f6
--- /dev/null
+++ b/docs/mkdocs.yml
@@ -0,0 +1,15 @@
+site_name: S.O. Conda
+
+theme:
+  name: "material"
+  features:
+    - navigation.expand
+    - navigation.path
+
+nav:
+  - Introduction: index.md
+  - Use and Customization: usage.md
+  - Installation: install.md
+  - Automated Deployment: automate.md
+  - Developer Notes: dev.md
+

From f7da3a171faa7e21550355fe5f922629670c81c4 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Thu, 31 Aug 2023 06:09:02 -0700
Subject: [PATCH 03/13] Switch back to miniforge installer.  Documentation
 updates.

---
 docs/docs/install.md        | 36 +++++++++++++++++--------
 soconda.sh                  | 10 +++----
 templates/modulefile_lua.in | 52 ++++++++++++++-----------------------
 templates/modulefile_tcl.in | 41 ++++++++++++++++++++++++++---
 tools/bootstrap_base.sh     | 42 +++++++++++++-----------------
 5 files changed, 104 insertions(+), 77 deletions(-)

diff --git a/docs/docs/install.md b/docs/docs/install.md
index 9ebb66a..3a26db8 100644
--- a/docs/docs/install.md
+++ b/docs/docs/install.md
@@ -25,15 +25,18 @@ clutter.
 ## Base Conda Environment
 
 If you already have a conda-forge base environment, then you can skip this
-step. Otherwise, decide on the install prefix for your overall conda
-environment. For this example, we will use `/opt/conda` as the path to the
-conda base installation. Now run the bootstrap script:
+step. However, you should consider setting the "solver" in the base environment
+to use libmamba. This will greatly speed up the dependency resolution
+calculation. Once you decide on the install prefix for your overall conda
+environment you can use the included bootstrap script. For this example, we
+will use `/opt/conda` as the path to the conda base installation. Now run the
+bootstrap script:
 
     $> ./tools/bootstrap_base "/opt/conda"
 
 This bootstrap will install a base system with the conda-forge channel set to
-the default. You can now source the conda initialization file and activate the
-base environment:
+the default and using the mamba solver. You can now source the conda
+initialization file and activate the base environment:
 
     $> source /opt/conda/etc/profile.d/conda.sh
     $> conda activate base
@@ -46,7 +49,7 @@ since it is done by the generated modulefile.
 By default, the conda package for mpi4py will be installed. This should work
 well for stand-alone workstations or single nodes. If you have a cluster with a
 customized MPI compiler, then set the `MPICC` environment variable to the MPI C
-compiler before creating an environment. That will cause the mpi4py package to
+compiler before running `soconda.sh`. That will cause the mpi4py package to
 be built using your compiler.
 
 ## Example:  Local System
@@ -71,14 +74,19 @@ Now we can load the module:
 
 ## Example:  NERSC
 
-At NERSC, the default provided python is from Anaconda, and does not work for
-our needs. Instead, we have a conda-forge base system installed in our project
-software directory:
+At NERSC, the default provided python is from Anaconda, and does not work well
+for our needs. Instead, we have a conda-forge base system installed in our
+project software directory:
 
     $> source /global/common/software/sobs/perlmutter/conda/etc/profile.d/conda.sh
     $> conda activate base
 
-Now we can either install a shared software environment or use this base environment to build a conda environment in a personal directory.  If you are installing to a shared software environment, you should do that as the project account and follow a specific naming convention which is beyond the scope of this document.  If you wanted to install these tools to your home directory you could do:
+Now we can either install a shared software environment or use this base
+environment to build a conda environment in a personal directory. If you are
+installing to a shared software environment, you should do that as the project
+account and follow a specific naming convention which is beyond the scope of
+this document. If you wanted to install these tools to your home directory you
+could do:
 
     $> ./soconda.sh -b ~/conda_envs -m ~/conda_envs/modulefiles
 
@@ -106,7 +114,7 @@ using this python stack.
 ## Customizing an Environment
 
 If you want to dramatically change the package versions / content of an
-`soconda` stack, just load the existing base conda environment and edit the
+`soconda` stack, just load the existing `base` conda environment and edit the
 three lists of packages (`packages_[conda|pip|local].txt`) to exclude certain
 packages or add extras. Then install it as usual.
 
@@ -130,6 +138,12 @@ interfaces, thread pinning, etc, when building packages that use OpenMP.
 We currently build pixell from source with the conda compilers for consistency,
 rather than installing the wheel.
 
+### Libactpol / Moby2
+
+There are three conda recipes for `libactpol_deps`, `libactpol`, and `moby2`.
+These are using git hashes that are either the latest or a branch / version
+recommended for S.O. use.
+
 ### So3g
 
 This package is currently installed from the wheel, but the conda package is
diff --git a/soconda.sh b/soconda.sh
index e074f04..ca6a7ec 100755
--- a/soconda.sh
+++ b/soconda.sh
@@ -127,9 +127,6 @@ if [ "x${env_check}" = "x" ]; then
     echo "channels:" >> "${CONDA_PREFIX}/.condarc"
     echo "  - conda-forge" >> "${CONDA_PREFIX}/.condarc"
     echo "changeps1: true" >> "${CONDA_PREFIX}/.condarc"
-    echo "channel_priority: strict" >> "${CONDA_PREFIX}/.condarc"
-    echo "envs_dirs:" >> "${CONDA_PREFIX}/.condarc"
-    echo "  - $(dirname ${CONDA_PREFIX})" >> "${CONDA_PREFIX}/.condarc"
     echo "env_prompt: '({name}) '" >> "${CONDA_PREFIX}/.condarc"
 
     # Reactivate to pick up changes
@@ -165,11 +162,10 @@ rm -f "${CONDA_PREFIX}/bin/cc"
 conda deactivate
 conda activate "${fullenv}"
 
-# Update conda and low-level tools, including pipgrip which we
+# Install low-level tools, including pipgrip which we
 # use to install dependencies of pip packages with conda.
-conda update --yes --all
-conda install --yes setuptools wheel anytree click packaging
-python3 -m pip install pipgrip
+conda install --yes --update-all setuptools pip wheel anytree click packaging
+pip install pipgrip
 
 mkdir -p "${CONDA_PREFIX}/conda-bld"
 conda-index "${CONDA_PREFIX}/conda-bld"
diff --git a/templates/modulefile_lua.in b/templates/modulefile_lua.in
index 3b4ccdc..06d1a23 100644
--- a/templates/modulefile_lua.in
+++ b/templates/modulefile_lua.in
@@ -23,39 +23,27 @@ conflict("sohpc", "so-env", "soconda", "python")
 -- This might be set by OS python and gives us problems.
 unsetenv("PYTHONSTARTUP")
 
--- Activate the conda environment by modifying the environment
--- directly.  This is needed since the source-sh and system
--- calls do not work.  This solution could be fragile, so should
--- be revisited in the future.
-
-setenv("CONDA_EXE", "@BASE@/bin/conda")
-setenv("CONDA_PYTHON_EXE", "@BASE@/bin/python")
-setenv("CONDA_PREFIX", "@ENVPREFIX@")
-setenv("CONDA_PROMPT_MODIFIER", "")
-setenv("CONDA_SHLVL", "1")
-setenv("CONDA_DEFAULT_ENV", "@ENVPREFIX@")
-prepend_path("PATH", "@ENVPREFIX@/bin")
-
-local funcs = "conda __conda_activate __conda_hashr __conda_reactivate __add_sys_prefix_to_path"
-
-execute{cmd="source " .. @BASE@ .. "/etc/profile.d/conda.sh; conda activate @ENVNAME@; export -f " .. funcs, modeA={"load"}}
-
-execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; pre=" .. conda_dir .. "; \
-	export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
-	export PATH=$(echo ${PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
-        unset -f " .. funcs .. "; \
-    unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\" | /bin/grep -v 'CONDA_ENVS_PATH\\|CONDA_PKGS_DIRS');", modeA={"unload"}}
-
-execute{cmd="source " .. conda_dir .. "/etc/profile.d/conda.sh; conda activate py${PYV}_${ENV}; export -f " .. funcs, modeA={"load"}}
-execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; pre=" .. conda_dir .. "; \
-	export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
-	export PATH=$(echo ${PATH} | tr ':' '\\n' | /bin/grep . | /bin/grep -v $pre | tr '\\n' ':' | sed 's/:$//'); \
-        unset -f " .. funcs .. "; \
-
-
--- Create a versioned user directory for local pip installation
+-- Versioned user directory for local pip installation
 local userbase = pathJoin(HOME, ".local", "soconda", "@VERSION@")
 setenv("PYTHONUSERBASE", userbase)
 local userbin = pathJoin(userbase, "bin")
-prepend_path("PATH", userbin)
+
+local funcs = "conda __conda_exe __conda_activate __conda_hashr __conda_reactivate"
+
+if (mode() == "load") then
+    execute{cmd="source " .. "@BASE@" .. "/etc/profile.d/conda.sh; \
+        conda activate @ENVNAME@; export -f " .. funcs .. \
+        "; export PATH=" .. userbin .. ":${PATH}", modeA={"load"}}
+end
+
+if (mode() == "unload") then
+    execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; \
+        pre=" .. "@BASE@" .. "; \
+        pipusr=" .. userbin .. "; \
+        export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | tr "\\n" ":" | sed 's/:$//'); \
+        export PATH=$(echo ${PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | /bin/grep -v $pipusr | tr "\\n" ":" | sed 's/:$//'); \
+        unset -f " .. funcs .. "; \
+        unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\");", modeA={"unload"}}
+end
+
 
diff --git a/templates/modulefile_tcl.in b/templates/modulefile_tcl.in
index e4e1f96..839c496 100644
--- a/templates/modulefile_tcl.in
+++ b/templates/modulefile_tcl.in
@@ -3,7 +3,6 @@
 ##   Simons Observatory Conda Environment.
 ##
 ##
-# variables for Tcl script use only
 set version  @VERSION@
 
 module-whatis "Loads conda tools for the Simons Observatory."
@@ -19,12 +18,48 @@ conflict sohpc so-env soconda python
 # Dependency module commands
 @MODLOAD@
 
+# This might be set by OS python and gives us problems.
+unsetenv PYTHONSTARTUP
+
+# Versioned user directory for local pip installation
+set userbase $env(HOME)/.local/soconda/@VERSION@
+setenv PYTHONUSERBASE $userbase
+set userbin $userbase/bin
+
+set funcs "conda __conda_exe __conda_activate __conda_hashr __conda_reactivate"
+
+# WIP: port lua techniques here...
+
+
+if {[module-info command load]} {
+    system "source @BASE@/etc/profile.d/conda.sh; \
+        conda activate @ENVNAME@; export -f $funcs .. \
+        "; export PATH=" .. userbin .. ":${PATH}"
+}
+
+if (mode() == "load") then
+    execute{cmd=, modeA={"load"}}
+end
+
+if (mode() == "unload") then
+    execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; \
+        pre=" .. "@BASE@" .. "; \
+        pipusr=" .. userbin .. "; \
+        export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | tr "\\n" ":" | sed 's/:$//'); \
+        export PATH=$(echo ${PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | /bin/grep -v $pipusr | tr "\\n" ":" | sed 's/:$//'); \
+        unset -f " .. funcs .. "; \
+        unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\");", modeA={"unload"}}
+end
+
+
+
+
+
 if {[module-info command unload]} {
     system AUTO_ACTIVATE_BASE=false @BASE@/bin/conda deactivate
 }
 
-# This might be set by OS python and gives us problems.
-unsetenv PYTHONSTARTUP
+
 
 # Activate the conda environment by modifying the environment
 # directly.  This is needed since the source-sh and system
diff --git a/tools/bootstrap_base.sh b/tools/bootstrap_base.sh
index d2f598f..41c733a 100755
--- a/tools/bootstrap_base.sh
+++ b/tools/bootstrap_base.sh
@@ -18,28 +18,22 @@ if [ "x${base}" = "x" ]; then
     exit 1
 fi
 
-
-if [ $(uname -s) = "Linux" ]; then
-    inst=$(eval "${scriptdir}/fetch_check.sh" https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname -s)-$(uname -m).sh miniforge.sh)
-else
-    if [ $(uname -s) = "Darwin" ]; then
-        inst=$(eval "${scriptdir}/fetch_check.sh" https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-$(uname -m).sh miniforge.sh)
-    else
-        echo "Unsupported operating system" >&2
-        exit 1
-    fi
-fi
-
-bash "${inst}" -b -f -p "${base}" \
-    && echo "# condarc for soconda" > "${base}/.condarc" \
-    && echo "channels:" >> "${base}/.condarc" \
-    && echo "  - conda-forge" >> "${base}/.condarc" \
-    && echo "channel_priority: strict" >> "${base}/.condarc" \
-    && echo "changeps1: true" >> "${base}/.condarc"
-
-# Activate and set solver.  Re-enable after mamba supports
-# strict channel order.
-# source "${base}/etc/profile.d/conda.sh"
-# conda install -n base conda-libmamba-solver
-# conda config --file "${base}/.condarc" --set solver libmamba
+inst=$(eval "${scriptdir}/fetch_check.sh" https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh miniforge.sh)
+
+bash "${inst}" -b -f -p "${base}"
+
+# Activate base and install libmamba solver
+source "${base}/etc/profile.d/conda.sh"
+conda activate base
+conda update -n base --yes conda
+conda install -n base --yes conda-libmamba-solver
+conda deactivate
+
+# Create base config file
+echo "# condarc bootstrapped by soconda" > "${base}/.condarc"
+echo "channels:" >> "${base}/.condarc"
+echo "  - conda-forge" >> "${base}/.condarc"
+echo "changeps1: true" >> "${base}/.condarc"
+echo "env_prompt: '({name}) '" >> "${base}/.condarc"
+echo "solver: libmamba" >> "${base}/.condarc"
 

From 1aaa3fafc18b696145cb225cc5970871c136644a Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Thu, 31 Aug 2023 07:43:28 -0700
Subject: [PATCH 04/13] More cleanup to tcl modulefile

---
 templates/modulefile_tcl.in | 46 ++-----------------------------------
 1 file changed, 2 insertions(+), 44 deletions(-)

diff --git a/templates/modulefile_tcl.in b/templates/modulefile_tcl.in
index 839c496..b6830f6 100644
--- a/templates/modulefile_tcl.in
+++ b/templates/modulefile_tcl.in
@@ -32,51 +32,9 @@ set funcs "conda __conda_exe __conda_activate __conda_hashr __conda_reactivate"
 
 
 if {[module-info command load]} {
-    system "source @BASE@/etc/profile.d/conda.sh; \
-        conda activate @ENVNAME@; export -f $funcs .. \
-        "; export PATH=" .. userbin .. ":${PATH}"
+    system "source @BASE@/etc/profile.d/conda.sh; conda activate @ENVNAME@; export -f ${funcs}; export PATH=${userbin}:${PATH}"
 }
 
-if (mode() == "load") then
-    execute{cmd=, modeA={"load"}}
-end
-
-if (mode() == "unload") then
-    execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; \
-        pre=" .. "@BASE@" .. "; \
-        pipusr=" .. userbin .. "; \
-        export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | tr "\\n" ":" | sed 's/:$//'); \
-        export PATH=$(echo ${PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | /bin/grep -v $pipusr | tr "\\n" ":" | sed 's/:$//'); \
-        unset -f " .. funcs .. "; \
-        unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\");", modeA={"unload"}}
-end
-
-
-
-
-
 if {[module-info command unload]} {
-    system AUTO_ACTIVATE_BASE=false @BASE@/bin/conda deactivate
+    system "for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; pre=@BASE@; pipusr=$userbin; export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | tr "\\n" ":" | sed 's/:$//'); export PATH=$(echo ${PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | bin/grep -v $pipusr | tr "\\n" ":" | sed 's/:$//'); unset -f ${funcs}; unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\");"
 }
-
-
-
-# Activate the conda environment by modifying the environment
-# directly.  This is needed since the source-sh and system
-# calls do not work.  This solution could be fragile, so should
-# be revisited in the future.
-
-setenv CONDA_EXE @BASE@/bin/conda
-setenv CONDA_PYTHON_EXE "@BASE@/bin/python"
-setenv CONDA_PREFIX "@ENVPREFIX@"
-setenv CONDA_PROMPT_MODIFIER ""
-setenv CONDA_SHLVL "1"
-setenv CONDA_DEFAULT_ENV "@ENVNAME@"
-prepend-path PATH "@ENVPREFIX@/bin"
-
-# Create a versioned location for user-installed pip packages.
-# Add this location to the start of the path.
-set userbase $env(HOME)/.local/soconda/@VERSION@
-setenv PYTHONUSERBASE $userbase
-prepend-path PATH $userbase/bin
-prepend-path PYTHONPATH $userbase/lib/python@PYVER@/site-packages

From c282e265fb69c2274392c536ab10a90e7ee6ff14 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Thu, 31 Aug 2023 13:05:01 -0700
Subject: [PATCH 05/13] More work on modulefiles

---
 templates/modulefile_lua.in | 10 +---------
 templates/modulefile_tcl.in |  7 ++-----
 2 files changed, 3 insertions(+), 14 deletions(-)

diff --git a/templates/modulefile_lua.in b/templates/modulefile_lua.in
index 06d1a23..999edfe 100644
--- a/templates/modulefile_lua.in
+++ b/templates/modulefile_lua.in
@@ -37,13 +37,5 @@ if (mode() == "load") then
 end
 
 if (mode() == "unload") then
-    execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; \
-        pre=" .. "@BASE@" .. "; \
-        pipusr=" .. userbin .. "; \
-        export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | tr "\\n" ":" | sed 's/:$//'); \
-        export PATH=$(echo ${PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | /bin/grep -v $pipusr | tr "\\n" ":" | sed 's/:$//'); \
-        unset -f " .. funcs .. "; \
-        unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\");", modeA={"unload"}}
+    execute{cmd="for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; pre=" .. "@BASE@" .. "; pipusr=" .. userbin .. "; export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr \":\" \"\\n\" | /bin/grep . | /bin/grep -v $pre | tr \"\\n\" \":\" | sed 's/:$//'); export PATH=$(echo ${PATH} | tr \":\" \"\\n\" | /bin/grep . | /bin/grep -v $pre | /bin/grep -v $pipusr | tr \"\\n\" \":\" | sed 's/:$//'); unset -f " .. funcs .. "; unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\");", modeA={"unload"}}
 end
-
-
diff --git a/templates/modulefile_tcl.in b/templates/modulefile_tcl.in
index b6830f6..3354552 100644
--- a/templates/modulefile_tcl.in
+++ b/templates/modulefile_tcl.in
@@ -28,13 +28,10 @@ set userbin $userbase/bin
 
 set funcs "conda __conda_exe __conda_activate __conda_hashr __conda_reactivate"
 
-# WIP: port lua techniques here...
-
-
 if {[module-info command load]} {
-    system "source @BASE@/etc/profile.d/conda.sh; conda activate @ENVNAME@; export -f ${funcs}; export PATH=${userbin}:${PATH}"
+   puts stdout "source @BASE@/etc/profile.d/conda.sh; conda activate @ENVNAME@; export -f ${funcs}; export PATH=${userbin}:\$PATH;"
 }
 
 if {[module-info command unload]} {
-    system "for i in $(seq ${CONDA_SHLVL:=0}); do conda deactivate; done; pre=@BASE@; pipusr=$userbin; export LD_LIBRARY_PATH=$(echo ${LD_LIBRARY_PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | tr "\\n" ":" | sed 's/:$//'); export PATH=$(echo ${PATH} | tr ":" "\\n" | /bin/grep . | /bin/grep -v $pre | bin/grep -v $pipusr | tr "\\n" ":" | sed 's/:$//'); unset -f ${funcs}; unset $(env | /bin/grep -o \"[^=]*CONDA[^=]*\");"
+    puts stdout "for i in \$(seq \${CONDA_SHLVL:=0}); do conda deactivate; done; pre=@BASE@; pipusr=${userbin}; export LD_LIBRARY_PATH=\$(echo \$LD_LIBRARY_PATH | tr \":\" \"\\n\" | /bin/grep . | /bin/grep -v \$pre | tr \"\\n\" \":\" | sed 's/:\$//'); export PATH=\$(echo \$PATH | tr \":\" \"\\n\" | /bin/grep . | /bin/grep -v \$pre | /bin/grep -v \$pipusr | tr \"\\n\" \":\" | sed 's/:\$//'); unset -f ${funcs}; unset \$(env | /bin/grep -o \"\[^=\]*CONDA\[^=\]*\");"
 }

From 74932285238ee0fa57f6ad82e9f3f4aab369c41a Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Thu, 21 Sep 2023 16:49:48 -0700
Subject: [PATCH 06/13] Fix lua modulefile.  Add explicit package dependency on
 openmp.

---
 pkgs/libactpol/meta.yaml      |  4 ++++
 pkgs/libactpol_deps/meta.yaml |  5 +++++
 pkgs/pixell/meta.yaml         | 10 +++++-----
 pkgs/toast/build.sh           |  1 -
 pkgs/toast/meta.yaml          |  3 ++-
 templates/modulefile_lua.in   |  7 +++----
 6 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/pkgs/libactpol/meta.yaml b/pkgs/libactpol/meta.yaml
index 65282ab..7e2690f 100644
--- a/pkgs/libactpol/meta.yaml
+++ b/pkgs/libactpol/meta.yaml
@@ -20,7 +20,11 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
+    - llvm-openmp >=4.0.1  # [osx]
+    - libgomp      # [linux]
   host:
+    - llvm-openmp >=4.0.1  # [osx]
+    - libgomp      # [linux]
     - openblas * openmp_*
     - automake
     - autoconf
diff --git a/pkgs/libactpol_deps/meta.yaml b/pkgs/libactpol_deps/meta.yaml
index b4bd46c..15ee4d5 100644
--- a/pkgs/libactpol_deps/meta.yaml
+++ b/pkgs/libactpol_deps/meta.yaml
@@ -21,8 +21,13 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('fortran') }}
+    - llvm-openmp >=4.0.1  # [osx]
+    - libgomp      # [linux]
   host:
+    - llvm-openmp >=4.0.1  # [osx]
+    - libgomp      # [linux]
     - openblas * openmp_*
+    - blas=*=*openblas
     - automake
     - autoconf
     - m4
diff --git a/pkgs/pixell/meta.yaml b/pkgs/pixell/meta.yaml
index 7d36fe6..82192d5 100644
--- a/pkgs/pixell/meta.yaml
+++ b/pkgs/pixell/meta.yaml
@@ -22,11 +22,10 @@ requirements:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - {{ compiler('fortran') }}
-    - llvm-openmp >=4.0.1  # [osx]
-    - libgomp      # [linux]
+    - llvm-openmp             # [(osx or linux)]
+    - _openmp_mutex * *_llvm  # [(osx or linux)]
   host:
-    - llvm-openmp >=4.0.1  # [osx]
-    - libgomp      # [linux]
+    - llvm-openmp             # [(osx or linux)]
     - openblas * openmp_*
     - automake
     - autoconf
@@ -43,8 +42,9 @@ requirements:
     - h5py
     - pillow
   run:
-    - python
+    - llvm-openmp             # [(osx or linux)]
     - openblas * openmp_*
+    - python
     - {{ pin_compatible('numpy') }}
     - scipy
     - astropy
diff --git a/pkgs/toast/build.sh b/pkgs/toast/build.sh
index ea32e4d..dd87bb1 100755
--- a/pkgs/toast/build.sh
+++ b/pkgs/toast/build.sh
@@ -21,7 +21,6 @@ cd build
 cmake \
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
     ${CMAKE_PLATFORM_FLAGS[@]} \
-    -DPYTHON_EXECUTABLE:FILEPATH="${PYTHON}" \
     -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
     -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
     -DCMAKE_PREFIX_PATH="${PREFIX}" \
diff --git a/pkgs/toast/meta.yaml b/pkgs/toast/meta.yaml
index 59464cb..1c4565c 100644
--- a/pkgs/toast/meta.yaml
+++ b/pkgs/toast/meta.yaml
@@ -27,8 +27,10 @@ requirements:
     - cmake
     - make                 # [unix]
     - llvm-openmp >=4.0.1  # [osx]
+    - libgomp      # [linux]
   host:
     - llvm-openmp >=4.0.1  # [osx]
+    - libgomp      # [linux]
     - python
     - fftw
     - openblas * openmp_*
@@ -37,7 +39,6 @@ requirements:
     - libaatm
     - libflac
   run:
-    - llvm-openmp >=4.0.1  # [osx]
     - python
     - {{ pin_compatible('fftw') }}
     - openblas * openmp_*
diff --git a/templates/modulefile_lua.in b/templates/modulefile_lua.in
index 999edfe..2d5c7b5 100644
--- a/templates/modulefile_lua.in
+++ b/templates/modulefile_lua.in
@@ -24,16 +24,15 @@ conflict("sohpc", "so-env", "soconda", "python")
 unsetenv("PYTHONSTARTUP")
 
 -- Versioned user directory for local pip installation
-local userbase = pathJoin(HOME, ".local", "soconda", "@VERSION@")
+local home = os.getenv("HOME")
+local userbase = pathJoin(home, ".local", "soconda", "@VERSION@")
 setenv("PYTHONUSERBASE", userbase)
 local userbin = pathJoin(userbase, "bin")
 
 local funcs = "conda __conda_exe __conda_activate __conda_hashr __conda_reactivate"
 
 if (mode() == "load") then
-    execute{cmd="source " .. "@BASE@" .. "/etc/profile.d/conda.sh; \
-        conda activate @ENVNAME@; export -f " .. funcs .. \
-        "; export PATH=" .. userbin .. ":${PATH}", modeA={"load"}}
+    execute{cmd="source " .. "@BASE@" .. "/etc/profile.d/conda.sh; conda activate @ENVNAME@; export -f " .. funcs .. "; export PATH=" .. userbin .. ":${PATH}", modeA={"load"}}
 end
 
 if (mode() == "unload") then

From a6831509c35d81342f0ce14df27bc398595ec5bb Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Thu, 21 Sep 2023 16:50:25 -0700
Subject: [PATCH 07/13] Restore test

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index cb77742..a4adfdb 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -62,7 +62,7 @@ jobs:
           conda activate "soconda_CI"
           export OMP_NUM_THREADS=2
           export MPI_DISABLE=1
-          #python3 -c 'import toast.tests; toast.tests.run()'
+          python3 -c 'import toast.tests; toast.tests.run()'
           git clone --depth=1 --single-branch --branch=master https://github.com/simonsobs/sotodlib.git
           pushd sotodlib
           python3 setup.py test

From 0dbc94eed63730ed9ca84e6b0ea930b90b85e9a1 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Mon, 25 Sep 2023 09:20:39 -0700
Subject: [PATCH 08/13] Clean up openmp dependencies

---
 .github/workflows/docs.yml    | 52 +++++++++++++++++++++++++++++++++++
 docs/docs/automate.md         | 21 ++++++++++++++
 docs/docs/install.md          |  9 +++---
 packages_conda.txt            |  2 +-
 packages_local.txt            |  2 +-
 packages_pip.txt              |  2 +-
 pkgs/libactpol/meta.yaml      | 10 +++++--
 pkgs/libactpol_deps/meta.yaml |  9 ++++--
 pkgs/moby2/meta.yaml          | 13 +++++----
 pkgs/pixell/meta.yaml         | 18 ++++++------
 pkgs/so3g/meta.yaml           | 20 +++++++-------
 pkgs/toast/build.sh           | 31 +++++++++++++++++----
 pkgs/toast/debug_lapack.patch | 14 ++++++++++
 pkgs/toast/meta.yaml          | 27 ++++++++++--------
 14 files changed, 176 insertions(+), 54 deletions(-)
 create mode 100644 .github/workflows/docs.yml
 create mode 100644 pkgs/toast/debug_lapack.patch

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 0000000..d601c9a
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,52 @@
+name:  Deploy Documentation
+
+# on:
+#   push:
+#     tags:
+#       - '*'
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  update_docs:
+    name: Build and Deploy Documentation
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+
+      - name: Create Cache ID
+        run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+
+      - name: Setup Cache
+        uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+
+      - name: Install Dependencies
+        run: |
+          pip install mkdocs mkdocstrings mkdocstrings-python mkdocs-material
+
+      - name: Deploy Docs
+        run: mkdocs gh-deploy --force
diff --git a/docs/docs/automate.md b/docs/docs/automate.md
index 6f36009..0f74e3e 100644
--- a/docs/docs/automate.md
+++ b/docs/docs/automate.md
@@ -1 +1,22 @@
 # Automating the Install
+
+The general process of automating the install proceeds like this:
+
+1. A cron job (or similar) runs periodically and launches a script which
+examines current tags of soconda and finds the latest one. It looks at the
+installation directory and determines whether this tag has been installed. If
+not, it runs an installation wrapper script for the current system.
+
+2. The wrapper script has hard-coded paths to the various locations and also
+knows how to build the version string to use. This script calls the
+`soconda.sh` script to install the latest tag.
+
+3. If a new tag was installed, a message is posted via slack hook to one of the
+Simons Observatory slack channels.
+
+## Example:  Perlmutter at NERSC
+
+In the `deploy` subdirectory are the relevant files. The perlmutter install
+wrapper script is in `install_perlmutter.sh`. The tag checking script run by
+the cron job is in `install_nersc_tag.sh`, and the example lines in the scron
+tab are in `scron_check_tag.slurm`.
diff --git a/docs/docs/install.md b/docs/docs/install.md
index 3a26db8..d87222f 100644
--- a/docs/docs/install.md
+++ b/docs/docs/install.md
@@ -35,8 +35,8 @@ bootstrap script:
     $> ./tools/bootstrap_base "/opt/conda"
 
 This bootstrap will install a base system with the conda-forge channel set to
-the default and using the mamba solver. You can now source the conda
-initialization file and activate the base environment:
+the default and using the libmamba solver. You can now source the conda
+initialization file and activate this base environment:
 
     $> source /opt/conda/etc/profile.d/conda.sh
     $> conda activate base
@@ -50,7 +50,7 @@ By default, the conda package for mpi4py will be installed. This should work
 well for stand-alone workstations or single nodes. If you have a cluster with a
 customized MPI compiler, then set the `MPICC` environment variable to the MPI C
 compiler before running `soconda.sh`. That will cause the mpi4py package to
-be built using your compiler.
+be built using your system MPI compiler.
 
 ## Example:  Local System
 
@@ -88,7 +88,8 @@ account and follow a specific naming convention which is beyond the scope of
 this document. If you wanted to install these tools to your home directory you
 could do:
 
-    $> ./soconda.sh -b ~/conda_envs -m ~/conda_envs/modulefiles
+    $> mkdir -p ~/conda_envs
+    $> ./soconda.sh -e ~/conda_envs/soconda -m ~/conda_envs/modulefiles
 
 And then load the module:
 
diff --git a/packages_conda.txt b/packages_conda.txt
index f928daf..29d0385 100644
--- a/packages_conda.txt
+++ b/packages_conda.txt
@@ -48,4 +48,4 @@ ipykernel
 # https://github.com/conda-forge/pyfftw-feedstock/issues/51
 pyfftw==0.12
 # Uncomment the next line if building so3g from source
-#boost
+boost
diff --git a/packages_local.txt b/packages_local.txt
index 52e41fa..f36d157 100644
--- a/packages_local.txt
+++ b/packages_local.txt
@@ -7,4 +7,4 @@ moby2
 toast
 # Uncomment next line to build so3g from source, and
 # comment out line in packages_pip.txt
-#so3g
+so3g
diff --git a/packages_pip.txt b/packages_pip.txt
index 8d5ef3f..1a20b56 100644
--- a/packages_pip.txt
+++ b/packages_pip.txt
@@ -2,6 +2,6 @@ qpoint
 pysm3
 # Uncomment here if installing wheel, and comment out
 # line in packages_local.txt
-so3g
+#so3g
 https://github.com/simonsobs/sotodlib/archive/master.tar.gz
 https://github.com/galsci/mapsims/archive/main.tar.gz
diff --git a/pkgs/libactpol/meta.yaml b/pkgs/libactpol/meta.yaml
index 7e2690f..db75357 100644
--- a/pkgs/libactpol/meta.yaml
+++ b/pkgs/libactpol/meta.yaml
@@ -20,12 +20,14 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
   host:
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - automake
     - autoconf
     - m4
@@ -39,9 +41,11 @@ requirements:
     - healpy
   run:
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
+    - {{ pin_compatible('libactpol_deps') }}
     - {{ pin_compatible('cfitsio') }}
     - {{ pin_compatible('wcslib') }}
-    - {{ pin_compatible('libactpol_deps') }}
 
 test:
   commands:
diff --git a/pkgs/libactpol_deps/meta.yaml b/pkgs/libactpol_deps/meta.yaml
index 15ee4d5..954dfdd 100644
--- a/pkgs/libactpol_deps/meta.yaml
+++ b/pkgs/libactpol_deps/meta.yaml
@@ -21,13 +21,14 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('fortran') }}
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
   host:
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
-    - blas=*=*openblas
+    - libblas * *openblas
+    - liblapack * *openblas
     - automake
     - autoconf
     - m4
@@ -36,6 +37,8 @@ requirements:
     - zziplib
   run:
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - {{ pin_compatible('zziplib') }}
 
 test:
diff --git a/pkgs/moby2/meta.yaml b/pkgs/moby2/meta.yaml
index 9a723e4..985077f 100644
--- a/pkgs/moby2/meta.yaml
+++ b/pkgs/moby2/meta.yaml
@@ -17,19 +17,18 @@ source:
 build:
   number: {{ build }}
   skip: true  # [win]
-  run_exports:
-    - moby2
 
 requirements:
   build:
     - {{ compiler('c') }}
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
-    - openblas * openmp_*
   host:
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - python
     - fftw
     - gsl
@@ -37,8 +36,10 @@ requirements:
     - numpy>=1.20
     - future
   run:
-    - python
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
+    - python
     - {{ pin_compatible('fftw') }}
     - {{ pin_compatible('gsl') }}
     - {{ pin_compatible('libactpol') }}
diff --git a/pkgs/pixell/meta.yaml b/pkgs/pixell/meta.yaml
index 82192d5..6757020 100644
--- a/pkgs/pixell/meta.yaml
+++ b/pkgs/pixell/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.19.0" %}
-{% set sha256 = "8142a2a368175de845166afffe3e4efd0ac0bdc109a96eb8f4cc0360e6191fd1" %}
+{% set version = "0.19.2" %}
+{% set sha256 = "aecc1bf6b2c6685d4641e76bdce40a4e4ed337cdffad69c294a9186ab8a5f9a1" %}
 
 {% set build = 0 %}
 
@@ -14,19 +14,20 @@ source:
 build:
   number: {{ build }}
   skip: true  # [win]
-  run_exports:
-    - pixell
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - {{ compiler('fortran') }}
-    - llvm-openmp             # [(osx or linux)]
-    - _openmp_mutex * *_llvm  # [(osx or linux)]
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   host:
-    - llvm-openmp             # [(osx or linux)]
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - automake
     - autoconf
     - m4
@@ -42,8 +43,9 @@ requirements:
     - h5py
     - pillow
   run:
-    - llvm-openmp             # [(osx or linux)]
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - python
     - {{ pin_compatible('numpy') }}
     - scipy
diff --git a/pkgs/so3g/meta.yaml b/pkgs/so3g/meta.yaml
index 71b15a0..41e21aa 100644
--- a/pkgs/so3g/meta.yaml
+++ b/pkgs/so3g/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.1.6" %}
-{% set sha256 = "50284e8f1c61a0488811791ce05941d5bdd1bd30ab61e2bf6a2f052c1f6cb059" %}
+{% set version = "0.1.8" %}
+{% set sha256 = "0e6d3e32af61524465892c575f92150bbc95aeb6e8349a1369cb013713cd8b7f" %}
 
 {% set build = 0 %}
 
@@ -20,32 +20,32 @@ build:
   script_env:
     - CFLAGS="-Wno-error -O3 -g -fPIC"
     - CXXFLAGS="-Wno-error -O3 -g -fPIC -std=c++14"
-  run_exports:
-    - so3g
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - cmake
-    - llvm-openmp >=4.0.1  # [osx]
+    - make         # [unix]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
-    - openblas * openmp_*
-    - make
   host:
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - python
     - numpy>=1.20
     - scipy
     - boost
     - libflac
   run:
+    - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - python
     - {{ pin_compatible('numpy') }}
-    - openblas * openmp_*
-    - {{ pin_compatible('liblapack') }}
     - {{ pin_compatible('boost') }}
     - {{ pin_compatible('libflac') }}
     - astropy
diff --git a/pkgs/toast/build.sh b/pkgs/toast/build.sh
index dd87bb1..1c87a4a 100755
--- a/pkgs/toast/build.sh
+++ b/pkgs/toast/build.sh
@@ -4,24 +4,45 @@ set -x
 
 declare -a CMAKE_PLATFORM_FLAGS
 if [[ ${HOST} =~ .*darwin.* ]]; then
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}")
-  # export LDFLAGS=$(echo "${LDFLAGS}" | sed "s/-Wl,-dead_strip_dylibs//g")
+    CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}")
+    # export LDFLAGS=$(echo "${LDFLAGS}" | sed "s/-Wl,-dead_strip_dylibs//g")
 else
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake")
+    CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake")
 fi
 
 if [[ ${DEBUG_C} == yes ]]; then
-  CMAKE_BUILD_TYPE=Debug
+    CMAKE_BUILD_TYPE=Debug
 else
-  CMAKE_BUILD_TYPE=Release
+    CMAKE_BUILD_TYPE=Release
 fi
 
+echo "DBG:  PATH=${PATH}"
+echo "DBG:  PYTHON=${PYTHON}"
+echo "DBG:  python3=$(which python3)"
+echo "DBG:  PY_VER=${PY_VER}"
+
 mkdir -p build
 cd build
 cmake \
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
     ${CMAKE_PLATFORM_FLAGS[@]} \
     -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
+    -DPython3_EXECUTABLE=$(which python3) \
+    -DPython3_INCLUDE_DIR="${PREFIX}/include/python${PY_VER}" \
+    -DPython3_FIND_VIRTUALENV=ONLY \
+    -DCMAKE_C_COMPILER="${CC}" \
+    -DCMAKE_CXX_COMPILER="${CXX}" \
+    -DCMAKE_C_FLAGS="-O3 -g -fPIC" \
+    -DCMAKE_CXX_FLAGS="-O3 -g -fPIC" \
+    -DCMAKE_VERBOSE_MAKEFILE=1 \
+    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+    -DCMAKE_PREFIX_PATH="${PREFIX}" \
+    -DFFTW_ROOT="${PREFIX}" \
+    -DAATM_ROOT="${PREFIX}" \
+    -DBLAS_LIBRARIES="${PREFIX}/lib/libblas${SHLIB_EXT}" \
+    -DLAPACK_LIBRARIES="${PREFIX}/lib/liblapack${SHLIB_EXT}" \
+    -DSUITESPARSE_INCLUDE_DIR_HINTS="${PREFIX}/include" \
+    -DSUITESPARSE_LIBRARY_DIR_HINTS="${LIBDIR}" \
     -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
     -DCMAKE_PREFIX_PATH="${PREFIX}" \
     "${SRC_DIR}"
diff --git a/pkgs/toast/debug_lapack.patch b/pkgs/toast/debug_lapack.patch
new file mode 100644
index 0000000..73511d8
--- /dev/null
+++ b/pkgs/toast/debug_lapack.patch
@@ -0,0 +1,14 @@
+diff -urN toast-3.0.0a19_orig/cmake/FindLAPACKnames.cmake toast-3.0.0a19/cmake/FindLAPACKnames.cmake
+--- toast-3.0.0a19_orig/cmake/FindLAPACKnames.cmake	2023-08-16 18:34:01.000000000 -0700
++++ toast-3.0.0a19/cmake/FindLAPACKnames.cmake	2023-09-22 09:51:26.249656186 -0700
+@@ -29,8 +29,8 @@
+               COMPILE_DEFINITIONS "-DLAPACK_${MANGLING}"
+               LINK_LIBRARIES "${LAPACK_LIBRARIES}" "${BLAS_LIBRARIES}" "${OMP_BLAS}"
+               OUTPUT_VARIABLE OUTPUT_MANGLING)
+-  # message("Test output for LAPACK_${MANGLING}:")
+-  # message(${OUTPUT_MANGLING})
++  message("Test output for LAPACK_${MANGLING}:")
++  message(${OUTPUT_MANGLING})
+   if(TRY_MANGLING)
+     set(LAPACK_NAMES "${MANGLING}")
+     break()
diff --git a/pkgs/toast/meta.yaml b/pkgs/toast/meta.yaml
index 1c4565c..95e996b 100644
--- a/pkgs/toast/meta.yaml
+++ b/pkgs/toast/meta.yaml
@@ -1,6 +1,6 @@
 
-{% set version = "3.0.0a18" %}
-{% set sha256 = "281d4c649cc5e2908ebbbe530dc85e2c86c7816827d102026cd084b7626b1f79" %}
+{% set version = "3.0.0a19" %}
+{% set sha256 = "e37c6e6de7a6829af378e0147113bd9439490cb5478be096c197fc6f7db6d6fe" %}
 
 {% set build = 0 %}
 
@@ -11,42 +11,45 @@ package:
 source:
   url: https://github.com/hpc4cmb/toast/archive/{{ version }}.tar.gz
   sha256: {{ sha256 }}
+  # patches:
+  #   - debug_lapack.patch
 
 build:
   skip: True  # [py<38]
   skip: True  # [win]
   number: {{ build }}
   string: "py{{ py }}h{{ PKG_HASH }}_{{ build }}"
-  run_exports:
-    - toast
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - cmake
-    - make                 # [unix]
-    - llvm-openmp >=4.0.1  # [osx]
+    - make         # [unix]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
   host:
-    - llvm-openmp >=4.0.1  # [osx]
+    - llvm-openmp  # [osx]
     - libgomp      # [linux]
+    - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - python
     - fftw
-    - openblas * openmp_*
-    - liblapack
     - suitesparse
     - libaatm
     - libflac
+    - numpy>=1.20
   run:
+    - openblas * openmp_*
+    - libblas * *openblas
+    - liblapack * *openblas
     - python
+    - {{ pin_compatible('numpy') }}
     - {{ pin_compatible('fftw') }}
-    - openblas * openmp_*
-    - {{ pin_compatible('liblapack') }}
     - {{ pin_compatible('suitesparse') }}
     - {{ pin_compatible('libaatm') }}
     - {{ pin_compatible('libflac') }}
-    - numpy>=1.20
     - scipy
     - matplotlib
     - astropy

From af12d2f817fff80bee07f9b2bea36d2cf4d681f0 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Mon, 25 Sep 2023 13:55:28 -0700
Subject: [PATCH 09/13] More work on consistent blas / openmp stack

---
 packages_conda.txt            | 14 +++++++++++---
 pkgs/libactpol/meta.yaml      |  2 ++
 pkgs/libactpol_deps/meta.yaml |  2 ++
 pkgs/moby2/meta.yaml          |  2 ++
 pkgs/pixell/meta.yaml         |  2 ++
 pkgs/so3g/meta.yaml           |  2 ++
 pkgs/toast/meta.yaml          |  2 ++
 soconda.sh                    |  2 +-
 8 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/packages_conda.txt b/packages_conda.txt
index 29d0385..2821425 100644
--- a/packages_conda.txt
+++ b/packages_conda.txt
@@ -1,10 +1,18 @@
 python=3.10.*
 compilers
-libopenblas=*=*openmp*
+# The LLVM openmp implementation is compatible with gcc
+# and fork-safe.
+_openmp_mutex=*=*_llvm
+#
+# Require the OpenBLAS + OpenMP flavor of linear algebra packages
+openblas=*=openmp_*
+libopenblas=*=openmp_*
 libblas=*=*openblas
+libcblas=*=*openblas
+liblapack=*=*openblas
+liblapacke=*=*openblas
+#
 conda-build
-libcblas
-blas-devel
 cmake
 autoconf
 automake
diff --git a/pkgs/libactpol/meta.yaml b/pkgs/libactpol/meta.yaml
index db75357..3e4c9d8 100644
--- a/pkgs/libactpol/meta.yaml
+++ b/pkgs/libactpol/meta.yaml
@@ -26,6 +26,7 @@ requirements:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - automake
@@ -41,6 +42,7 @@ requirements:
     - healpy
   run:
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - {{ pin_compatible('libactpol_deps') }}
diff --git a/pkgs/libactpol_deps/meta.yaml b/pkgs/libactpol_deps/meta.yaml
index 954dfdd..17f6ccf 100644
--- a/pkgs/libactpol_deps/meta.yaml
+++ b/pkgs/libactpol_deps/meta.yaml
@@ -27,6 +27,7 @@ requirements:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - automake
@@ -37,6 +38,7 @@ requirements:
     - zziplib
   run:
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - {{ pin_compatible('zziplib') }}
diff --git a/pkgs/moby2/meta.yaml b/pkgs/moby2/meta.yaml
index 985077f..c1df12e 100644
--- a/pkgs/moby2/meta.yaml
+++ b/pkgs/moby2/meta.yaml
@@ -27,6 +27,7 @@ requirements:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - python
@@ -37,6 +38,7 @@ requirements:
     - future
   run:
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - python
diff --git a/pkgs/pixell/meta.yaml b/pkgs/pixell/meta.yaml
index 6757020..2f949f8 100644
--- a/pkgs/pixell/meta.yaml
+++ b/pkgs/pixell/meta.yaml
@@ -26,6 +26,7 @@ requirements:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - automake
@@ -44,6 +45,7 @@ requirements:
     - pillow
   run:
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - python
diff --git a/pkgs/so3g/meta.yaml b/pkgs/so3g/meta.yaml
index 41e21aa..218cc8d 100644
--- a/pkgs/so3g/meta.yaml
+++ b/pkgs/so3g/meta.yaml
@@ -33,6 +33,7 @@ requirements:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - python
@@ -42,6 +43,7 @@ requirements:
     - libflac
   run:
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - python
diff --git a/pkgs/toast/meta.yaml b/pkgs/toast/meta.yaml
index 95e996b..2acd1f9 100644
--- a/pkgs/toast/meta.yaml
+++ b/pkgs/toast/meta.yaml
@@ -32,6 +32,7 @@ requirements:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - python
@@ -42,6 +43,7 @@ requirements:
     - numpy>=1.20
   run:
     - openblas * openmp_*
+    - libopenblas * openmp_*
     - libblas * *openblas
     - liblapack * *openblas
     - python
diff --git a/soconda.sh b/soconda.sh
index ca6a7ec..2ad30fd 100755
--- a/soconda.sh
+++ b/soconda.sh
@@ -203,7 +203,7 @@ while IFS='' read -r line || [[ -n "${line}" ]]; do
         conda-build ${pkgrecipe} > "log_${pkgname}" 2>&1
         cat "log_${pkgname}"
         echo "Installing local package '${pkgname}'"
-        conda install --yes --use-local --no-deps ${pkgname}
+        conda install --yes --use-local ${pkgname}
     fi
 done < "${scriptdir}/packages_local.txt"
 

From d1cf0770d435ba5aea54b639ee4d52b2eef7e011 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Mon, 25 Sep 2023 15:41:03 -0700
Subject: [PATCH 10/13] Default to using so3g wheel for now

---
 packages_conda.txt | 2 +-
 packages_local.txt | 6 ++++--
 packages_pip.txt   | 2 +-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/packages_conda.txt b/packages_conda.txt
index 2821425..662f5ef 100644
--- a/packages_conda.txt
+++ b/packages_conda.txt
@@ -56,4 +56,4 @@ ipykernel
 # https://github.com/conda-forge/pyfftw-feedstock/issues/51
 pyfftw==0.12
 # Uncomment the next line if building so3g from source
-boost
+#boost
diff --git a/packages_local.txt b/packages_local.txt
index f36d157..c52b269 100644
--- a/packages_local.txt
+++ b/packages_local.txt
@@ -6,5 +6,7 @@ moby2
 # and move to packages_conda.txt
 toast
 # Uncomment next line to build so3g from source, and
-# comment out line in packages_pip.txt
-so3g
+# comment out line in packages_pip.txt.  NOTE: this
+# requires addressing pysqlite3-wheels and qpoint
+# dependencies.
+#so3g
diff --git a/packages_pip.txt b/packages_pip.txt
index 1a20b56..8d5ef3f 100644
--- a/packages_pip.txt
+++ b/packages_pip.txt
@@ -2,6 +2,6 @@ qpoint
 pysm3
 # Uncomment here if installing wheel, and comment out
 # line in packages_local.txt
-#so3g
+so3g
 https://github.com/simonsobs/sotodlib/archive/master.tar.gz
 https://github.com/galsci/mapsims/archive/main.tar.gz

From 191a3835a76642617b5ba57b60e0897bff18edf8 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Mon, 25 Sep 2023 15:51:25 -0700
Subject: [PATCH 11/13] Add badges for documentation and test build

---
 .github/workflows/docs.yml |   4 +-
 README.md                  | 203 +------------------------------------
 2 files changed, 6 insertions(+), 201 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index d601c9a..cb1fc4c 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -49,4 +49,6 @@ jobs:
           pip install mkdocs mkdocstrings mkdocstrings-python mkdocs-material
 
       - name: Deploy Docs
-        run: mkdocs gh-deploy --force
+        run: |
+          cd docs
+          mkdocs gh-deploy --force
diff --git a/README.md b/README.md
index 0bd4edc..c429d53 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+![Documentation building status](https://github.com/simonsobs/soconda/actions/workflows/docs.yml/badge.svg) ![Latest test build](https://github.com/simonsobs/soconda/actions/workflows/test.yml/badge.svg)
+
 # Simons Observatory Conda Tools
 
 This repository contains scripts to help with:
@@ -10,204 +12,5 @@ This repository contains scripts to help with:
 
 - Creating a versioned modulefile for loading the environment
 
-## Using an Existing Environment
-
-If you are just using an already-created environment, you can follow
-instructions on project resources (Confluence) for how to load a particular
-version on a system. After loading an environment, there are a several ways to
-customize things.
-
-### Overriding a Few Packages
-
-Each `soconda` modulefile sets the user directory (for `pip install --user`) to
-be in a versioned location in your home directory. If you want to use a
-different / newer version of `sotodlib` (for example), then you can just do:
-
-    $> pip install --user https://github.com/simonsobs/sotodlib/archive/master.tar.gz
-
-If you swap to a different `soconda` environment, your user package install
-directory will also switch.
-
-### More Extensive Customization
-
-One benefit of an `soconda` environment is that it also contains conda packages
-built for some legacy compiled tools. If you want to keep those, but
-dramatically change which other conda packages are installed, you can first
-create a new personal environment while cloning an existing one:
-
-    $> conda create --clone soconda_20230809_1.0.0 /path/to/my/env
-
-Then activate your new environment and conda install whatever you like:
-
-    $> conda activate /path/to/my/env
-    $> conda install foo bar blat
-
-Note that your pip user directory will still be set to the location created by
-the original upstream module, and you can also "`pip install --user`"
-additional packages to go with your custom conda environment.
-
-### Rolling Your Own
-
-You can also just load a conda base environment on a particular system and then
-read the rest of this document to install your own environment. You can edit
-the files:
-
-    packages_conda.txt
-    packages_local.txt
-    packages_pip.txt
-
-to control which packages will be installed with conda, pip, or built locally.
-
-## Creating a Simons Observatory Environment
-
-The install script takes options to specify the location of the base environment
-(if it is not already activated) and the name (or full path) of the environment
-to create. It also allows specifying a central location to install the
-modulefile.
-
----
-**NOTE**
-
-Running the `soconda.sh` script will create log files and downloaded sources in
-the current directory. Consider running the command from within a temporary
-build directory to avoid clutter.
-
----
-
-### Base Conda Environment
-
-If you already have a conda-forge base environment, then you can skip this
-step. Otherwise, decide on the install prefix for your overall conda
-environment. For this example, we will use `/opt/conda` as the path to the
-conda base installation. Now run the bootstrap script:
-
-    $> ./tools/bootstrap_base "/opt/conda"
-
-This bootstrap will install a base system with the conda-forge channel set to
-the default. You can now source the conda initialization file and activate the
-base environment:
-
-    $> source /opt/conda/etc/profile.d/conda.sh
-    $> conda activate base
-
-After installing an `soconda` environment below, the resulting module file will
-do this on load.
-
-### Special Note on mpi4py
-
-By default, the conda package for mpi4py will be installed using the mpich
-flavor. This should work well for stand-alone workstations or single nodes. If
-you have a cluster with a customized MPI compiler, then set the `MPICC`
-environment variable to the MPI C compiler before creating an environment. That
-will cause the mpi4py package to be built using your compiler.
-
-### Example:  Local System
-
-Starting from scratch, bootstrap a small conda-forge base environment in `~/conda`:
-
-    $> ./tools/bootstrap_base.sh ~/conda
-    $> source ~/conda/etc/profile.d/conda.sh
-    $> conda activate base
-
-Create an `soconda` environment with default name and version. However, we
-decide to put all the modulefiles into a central location in the root of the
-base conda install:
-
-    $> ./soconda.sh -b ~/conda -m ~/conda/modulefiles
-
-Now we can load the module:
-
-    $> module use ~/conda/modulefiles
-    $> module avail
-    $> module load soconda/XXXXXX
-
-### Example:  NERSC
-
-At NERSC, the default provided python is from Anaconda, and cannot be easily
-customized for our needs. Instead, we have a conda-forge base system installed
-in our project software directory:
-
-    $> source /global/common/software/sobs/perlmutter/conda/etc/profile.d/conda.sh
-    $> conda activate base
-
-Now we can either install a shared software environment or use this base environment to build a conda environment in a personal directory.
-
-## Loading an Environment
-
-The created conda environment includes the root "name" (or path) specified at
-creation time and has the version appended to this. For example, if you did not
-specify the name or the version, then it would have created an environment under
-`envs/soconda_<git version>`.
-
-### Loading an Environment with a Modulefile
-
-There is a module file installed with each soconda environment. If you
-specified the module directory during install, then a module named after the
-version was created in that directory. The module file will initialize the
-conda base environment and then activate the environment you created.
-
-Ensure that the location of the modulefile is in your search path:
-
-    # (If you specified a custom module file directory)
-    $> module use /path/to/custom/modulefiles
-
-    # OR (you are using the defaults, and your base install is in /opt/conda)
-    $> module use /opt/conda/envs/soconda_1.0.0/modulefiles
-
-And then load the module:
-
-    $> module load soconda/1.0.0
-
-Doing a `module unload soconda` will deactivate the conda environment and
-remove any conda initialization from your shell environment.
-
-### Running Tests
-
-After loading an `soconda` environment, you can run some tests with:
-
-    $> ./run_tests.sh
-
-## Customizing an Environment
-
-If you want to dramatically change the package versions / content of an
-`soconda` stack, just load the existing base conda environment and edit the
-three lists of packages (`packages_[conda|pip|local].txt`) to exclude certain
-packages or add extras. Then install it to some personal location outside the
-base install (i.e. pass the full path to `soconda -e <path>`).
-
-## Deleting an Environment
-
-The `soconda` environments are self contained and you can delete them by
-removing the path or (if using a name), removing the
-`<base dir>/envs/<name of env>` directory. You can optionally delete the
-modulefile and the pip local directory in your home directory.
-
-## Advanced Details
-
-The compiled packages assume the use of the conda compilers for consistency with
-the libraries installed through conda. If you want to change those compilers you
-can remove the `compilers` conda package and manually set the `CC`, `CXX`, and `FC`
-environment variables. Full warning that this may cause problems with threading
-interfaces, thread pinning, etc, when building packages that use OpenMP.
-
-### Pixell
-
-We currently build pixell from source with the conda compilers for consistency,
-rather than installing the wheel.
-
-### So3g
-
-This package is currently built from source by default, but the pre-built wheel
-(which comes bundled with OpenMP-enabled libopenblas) should also work. To use
-that, comment out the so3g line in `packages_local.txt` and uncomment the
-line in `packages_pip.txt`.
-
-### TOAST
-
-This package is currently built from source by default, with dependencies
-installed through conda. When toast-3.0 arrives in the conda-forge toast
-feedstock, it should be added back to `packages_conda.txt`. It should also work
-to install the python wheel package by commenting out the toast entry in
-`packages_local.txt` and adding it to `packages_pip.txt`.
-
+## [Full Documentation](https://simonsobs.github.io/soconda/)
 

From a78d0c8f60dc473ef96a67a3ec08955d3bde9c67 Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Mon, 25 Sep 2023 15:58:09 -0700
Subject: [PATCH 12/13] Try to fix docs deploy from action

---
 .github/workflows/docs.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index cb1fc4c..d5ee518 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -47,6 +47,8 @@ jobs:
       - name: Install Dependencies
         run: |
           pip install mkdocs mkdocstrings mkdocstrings-python mkdocs-material
+          git config user.name 'github-actions[bot]'
+          git config user.email 'github-actions[bot]@users.noreply.github.com'
 
       - name: Deploy Docs
         run: |

From dbd993e9728edd144249421b7131515e09e52dbb Mon Sep 17 00:00:00 2001
From: Theodore Kisner <tskisner.public@gmail.com>
Date: Mon, 25 Sep 2023 16:06:37 -0700
Subject: [PATCH 13/13] Add link from docs back to site

---
 docs/docs/index.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/docs/index.md b/docs/docs/index.md
index c757ece..5bea652 100644
--- a/docs/docs/index.md
+++ b/docs/docs/index.md
@@ -1,6 +1,7 @@
 # Simons Observatory Conda Tools
 
-This repository contains scripts to help with:
+[This git repository](https://github.com/simonsobs/soconda) contains scripts to
+help with:
 
 - Installing a conda base system (optional)