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the CaHVA and CaLVA begin and end are set according to the specific morphology, these shouldn't have default values
Filtering parameterfiles by content is wise for speedup and ensuring you only get unique parameterfiles, but it only really makes sense if you do "hash_rename" copy method for parameterfiles. If you use "remount", you want parameterfiles to preserve their different filenames, independent of whether or not they may be identical in content. Otherwise, rerun_db throws an error when it reruns e.g. a sim_trial_index that has a paramfile with mismatching filename (but identical content) to the paramfile it is looking for.
…iles When rerunning simulation trials from databases, the .syn and .con files referenced in network param files will contain relative db paths. these should be resolved when parsing the re-runned simulation trials to a new database
…ll other paramfiles)
This PR proposes some changes that address some minor friction I encountered running `RW` on the pyloric model. Most are minor, but I'd love some extra eyes on nr 5 1. Isolate `RW` as a separate package by removing dependency on `data_base.utils.silence_stdout` (80a45da and 47b41ef) 2. Fix a pandas API change for newer versions of pandas: initializing a `DataFrame` from a list of `dict`s need to be done with `concat`, not the `DataFrame` initializer. Sure I guess. (b6b1c82) 3. Remove unused imports (990c853) 4. Expand documentation: the evaluation function needs to return the parameters as part of the evaluation. I didn't know this, and it wasn't in the docs, so I just added it to the docs. (a61bc76, [15c99fb](15c99fb), [7533fef](7533fef)) 5. Make a clearer distinction between `params_to_explore` and `all_param_names` during `run_RW`. For more details, see explanation of commit 0839ca8. I needed to change this to run pyloric simulations, since they contain a random seedpoint that had to remain fixed, but was nonetheless part of the parameter vector.
iteritems was useful in Py2, but pretty much deprecated in newer versions of py3, which usees generators by default
Forgot the reason why :( But is necessary
…¿? (#459) For some reason, data_base._version has a string formatting that does not work for me. This just fixes the string formatting
- add `get_kernel_dict` to `Strategy_spatiotemporalRaisedCosine` (ec51ce1) - Cast some things to list Forgot the reason why :( But is necessary (594e7fb) - use items instead of iteritems, iteritems was useful in Py2, but pretty much deprecated in newer versions of py3, which usees generators by default (c6c4933) - Cast things that need to be int to int (392c665) - Recurse keys in subdatabases (937f480)
# Bug fixes 96f34fe (develop) Bugfix reduced model (#460) 5964529 bugfix: data_base._version had a weird string formatting bug somehow?¿? (#459) ## Test suite 3d404d1 Fix `dbr` tests d137d11, a80c4bc Make notebook mode optional in test suite # Features ## Exploration algorithm dcbd3cf merge su_202602 (#457) d4ec7df Refactor Exploration (#458) 0839ca8 Logically separate params needed for simulation and `params_to_explore` in `run_RW` `run_RW` tends to pass around `params_to_explore`, which is not necessarily all parameters needed for a simulation. This is fine. However, the initial param seed was index _only_ on `params_to_explore`. This is not necessarily all params needed for simulation. b6b1c82 Use 'pd.concat' to build dataframe from list of dictionaries. Newer pandas API does not allow initializing a DataFrame from a list of dictionaries anymore, favoring an explicit call to `concat` instead. 39fdabe Don't cast `all_param_names` to list All downstream API works when leaving the `all_param_names = param_ranges.index` as a `pd.Index`. It's only ever used for indexing and counting the length. By not casting it to a list, you also support `MultiIndex` parameters (like the pyloric simulations). If you cast to a `list`, pandas gets angry and claims it does not know how to interpret a lis of tuples as an `Index`. ## SWC exporter caa795c Merge branch 'swc' into develop 0347c7c [feat] Add swc converter for cell No reader (yet) # Improvements 18bef9e, 2ae29f8 Improved error handling for cmiv fed952f Use `conda-forge` distribution of `pyarrow` a2f5280 [feat] Better/more verbose error handling in compiling mechanisms 3daf3ec [minor] more descriptive variable names in `Simulator.get_simulated_cell`
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
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Roadmap
dRWfrom su (see Su 202602 #457)Environment
NEURON is pinned down to <9.0 on macOS. The NEURON 9.0 update translates
.modfiles to C++ rather than C. This breaks some of our.modfiles,as they have duplicate function definitions. Allowed (but recommended
against) in C, disallowed in C++.
(ecd7d14).
Astroid is pinned down. Newer versions of astroid break our older
version of Sphinx, and filenames get mangled
(ada6784)
Pin down g++ and use the conda-distributed version on Linux to avoid
using too-new g++ on very new systems
(49a44e2)
Bug fixes
Fix: initializing other people's register. Logical bug in assuming the
database register is always your own (it's not)
(7bc4baf)
Fix: allow fetching
ModelDataBases by unique ID(b5d95d2)
Fix faulty
sim_trial_indexfor dendritic voltage traces(81723e1)
Fix: Only filter paramfiles during
simrun_init_dbwhenhash_renameis True (afc4968)
Fix: resolve relative
.synand.confiles(81723e1)
Minor changes
Internal reflinking to function and class arguments now works. not all
:param:roles have a valid FQN yet though.Improve wording in documentation
Fix typo's
Update reflink to NEURON documentation
Escape backslashes, underscores and asterisks in docstsrings