Alex Lubbock
Alex Lubbock
Currently, slapd listens on ldap:/// and ldapi:/// during bootstrapping, which means that external connections to the container can get accepted before the bootstrapping is complete. This causes issues when using...
The pqchecker download URL redirects to HTTPS, but the TLS certificate is only valid for meddeb.net at the time of writing (without the www. prefix), so curl fails. This PR...
I'm getting a non-zero exit code when all tests either pass or are skipped. Using Miniconda on Appveyor/Windows 64bit/Python 3.6/nose 1.3.7. The exact error looks like: ``` nosetests build/lib/pysb -a...
In BNG, a compartment applied to a complex is distinct from one applied to a monomer, by use of prefix and postfix notation. In PySB, one can use parentheses to...
In rare situations, when BNG outputs a lot of data to STDOUT quickly and fills the buffer, PySB could lockup due to how subprocess handles reading pipe buffers. The only...
As reported by @acorbat on [gitter](https://gitter.im/pysb/pysb?at=5e85066855d0d07c2d2f46c0), the `catalyze_complex` macro fails with a `DanglingBondError` in the following example, presumably due to the use of a dimer as a substrate: ```python from...
Python 2.x support will end on 01/01/20. Many packages are [pledging](https://python3statement.org/) to remove Python 2 support by then, or even sooner. I propose we aim to remove Python 2 support...
`pysb.bng.run_ssa`'s functionality is a subset of `pysb.simulator.BngSimulator`. We should remove the former as part of the 2.0 API simplification. See also the issues around `return` format documentation and incongruities between...
While there is [module-level documentation](http://docs.pysb.org/en/stable/modules/simulator.html) for `pysb.simulator`, some examples in the tutorial would help new users.
Generator code (for BNG and Kappa) is currently stored under `pysb/generator/`. It could either be moved into the relevant `pysb/export/` files, or into the relevant interfaces directly (`pysb/bng.py` and `pysb/kappa.py`)....