Release cycle, December 2024

[pearsonca]

Bug Fixes:

• The HPC init script no longer fails if a conda environment is already active, Deactivate Conda Env In HPC Init Script #388.
• Stdout/stderr from flepimop-inference-slot called by flepimop-inference-main are piped to a log file via system2 instead of pipes to support MINGW64, modified to capture stdout and stderr to log in using system2() being… #289.

Dependencies:

• click minimum is now 8.1.7 (latest as of Aug 17, 2023).
• Added missing h5py dependency to gempyor requirements and specified dask dependency to include dataframe optional dependencies, Convert setup.cfg To pyproject.toml #391.

Deprecates:

• gempyor-simulate ... in favor of flepimop simulate ....
• Soft deprecated the -c/--config_files option (config file(s) are now arguments not options).

New Features:

• Basic support for multiple config files
• A patch command that takes multiple config files and yields the merged result
• Converted gempyor's setup.cfg to the more modern pyproject.toml, Convert setup.cfg To pyproject.toml #391. No user facing changes.
• Added flepimop modifiers subcommand with one action, config-plot, for plotting the effects of modifiers on a config, Merge emcee_batch Into dev #404.

Removes/Modifies:

• gempyor-(seir|outcomes) ... - these were already no longer supported, just pruning entry points

[pearsonca]

I'm seeing one potential issue w/ switch to pyproject.toml when using manual pip install -e ...:

ERROR: Project flepimop/gempyor_pkg has a 'pyproject.toml' and its build backend is missing the 'build_editable' hook.
Since it does not have a 'setup.py' nor a 'setup.cfg', it cannot be installed in editable mode.
Consider using a build backend that supports PEP 660.

also installation indicates:

Building wheels for collected packages: UNKNOWN
  Building wheel for UNKNOWN (pyproject.toml) ... done
  Created wheel for UNKNOWN: filename=UNKNOWN-0.0.0-py3-none-any.whl size=961 sha256=8943442efaf1aac39f15f144d25a48042ce1d647164abc117d65096b5e0585d6
  Stored in directory: /tmp/pip-ephem-wheel-cache-zxe25xtv/wheels/95/8c/e2/0b81714075ce5a6ffb5f7b3799c8899d09486f0b2b5b467e71
Successfully built UNKNOWN
Installing collected packages: UNKNOWN
Successfully installed UNKNOWN-0.0.0

Seems like some meta-data missing here?

pip version 24.3.1, python version 3.10.12

[TimothyWillard]

I'm seeing one potential issue w/ switch to pyproject.toml when using manual pip install -e ...:

I'm having a difficult time replicating this one.

twillard@Mac ~/D/G/H/flepiMoP (dev)> uv venv .venv --python=/opt/homebrew/bin/python3.10
Using Python 3.10.16 interpreter at: /opt/homebrew/opt/[email protected]/bin/python3.10
Creating virtualenv at: .venv
Activate with: source .venv/bin/activate.fish
twillard@Mac ~/D/G/H/flepiMoP (dev)> source .venv/bin/activate.fish
(.venv) twillard@Mac ~/D/G/H/flepiMoP (dev)> uv pip install 'pip==24.3.1'
Resolved 1 package in 171ms
Prepared 1 package in 184ms
Installed 1 package in 7ms
 + pip==24.3.1
(.venv) twillard@Mac ~/D/G/H/flepiMoP (dev)> python --version
Python 3.10.16
(.venv) twillard@Mac ~/D/G/H/flepiMoP (dev)> pip --version
pip 24.3.1 from /Users/twillard/Desktop/GitHub/HopkinsIDD/flepiMoP/.venv/lib/python3.10/site-packages/pip (python 3.10)
(.venv) twillard@Mac ~/D/G/H/flepiMoP (dev)> pip install --editable flepimop/gempyor_pkg[test,aws]
Obtaining file:///Users/twillard/Desktop/GitHub/HopkinsIDD/flepiMoP/flepimop/gempyor_pkg
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done
.....

The output Building wheels for collected packages: UNKNOWN seems suspicious to me, what is the output of pwd and what is the full install command being used?

[pearsonca]

The output Building wheels for collected packages: UNKNOWN seems suspicious to me, what is the output of pwd and what is the full install command being used?

$ pwd
> /home/holism/workspaces/flepiMoP
$ sudo pip install -e flepimop/gempyor_pkg/

curiously, does not barf when not sudoing, also the "UNKNOWN" issue disappears.

clearly, i should just not do system-wide library installs.

[TimothyWillard]

The last remaining item for this release is GH-423. After that we will be clear to review and merge.