-
Notifications
You must be signed in to change notification settings - Fork 14
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #139 from esi-neuroscience/acme_amputation
Acme amputation. Unanesthetized.
- Loading branch information
Showing
40 changed files
with
1,699 additions
and
1,546 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| # Changelog of SyNCoPy | ||
| All notable changes to this project will be documented in this file. | ||
|
|
||
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), | ||
| and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
|
|
||
| ## [Unreleased] | ||
| ### NEW | ||
| - Made SyNCoPy PEP 517 compliant: added pyproject.toml and modified setup.py | ||
| accordingly | ||
| - Added IBM POWER testing pipeline (via dedicated GitLab Runner) | ||
| - Added Superlet spectral estimation method | ||
|
|
||
| ### CHANGED | ||
|
|
||
| ### REMOVED | ||
| - Retired tox in `slurmtest` CI pipeline in favor of a "simple" pytest testing | ||
| session due to file-locking problems of tox environments on NFS mounts | ||
|
|
||
| ### DEPRECATED | ||
| - Removed ACME from source repository: the submodule setup proved to be too | ||
| unreliable and hard to maintain. ACME is now an optional (but recommended) | ||
| dependency of SyNCoPy | ||
|
|
||
| ### FIXED | ||
| - Stream-lined GitLab Runner setup: use cluster-wide conda instead of local | ||
| installations (that differ slightly across runners) and leverage `tox-conda` | ||
| to fetch pre-built dependencies | ||
|
|
||
| ## [v0.1b2] - 2020-01-15 | ||
| Housekeeping and maintenance release | ||
|
|
||
| ### NEW | ||
| - Included ACME as SyNCoPy submodule: all ESI-HPC cluster specific code has | ||
| been migrated to the new ACME package, see https://github.com/esi-neuroscience/acme | ||
| - Better late than never: added this CHANGELOG file | ||
|
|
||
| ### CHANGED | ||
| - Modified GitLab CI Pipeline Setup + version handling: use `setuptools_scm` | ||
| to populate `spy.__version__` instead of hard-coding a version string | ||
| in the package `__init__.py`; this makes test-uploads to PyPI-Test infinitely | ||
| easier since `setuptools_scm` takes care of generating non-conflicting | ||
| package versions. | ||
| - Modified packaging setup and adapted modular layout to account for new | ||
| submodule ACME | ||
|
|
||
| ### REMOVED | ||
| - Deleted ESI-specific `dask_helpers.py` module (migrated to ACME) | ||
|
|
||
| ### DEPRECATED | ||
| - Cleaned up dependencies: removed all `jupyter`-packages from depencency | ||
| list to not cause (unnecessary) conflicts in existing Python environments | ||
|
|
||
| ### FIXED | ||
| - Repaired CI pipelines | ||
| - Repaired h5py version mismatch: pin SyNCoPy to `hypy` versions greater than | ||
| 2.9 but less than 3.x | ||
| - Pin SyNCoPy to Python 3.8.x (Python 3.9 currently triggers too many dependency | ||
| conflicts) | ||
|
|
||
| ## [v0.1b1] - 2020-10-23 | ||
| First public pre-release of SyNCoPy on PyPI and GitHub. | ||
|
|
||
| ### NEW | ||
| - Included `selectdata` as a `computeFunction` that uses the parallelization | ||
| framework in `ComputationalRoutine` to perform arbitrary data-selection tasks | ||
| (including but not limited to unordered lists, repetitions and removals). | ||
| - Included time-frequency analysis routines `mtmconvol` and `wavelet` | ||
| - Added plotting functionality: functions `singlepanelplot` and `multiplanelplot` | ||
| allow quick visual inspection of `AnalogData` and `SpectralData` objects | ||
| - Added support to process multiple SyNCoPy objects in a single meta-function | ||
| call (all decorators have been modified accordingly) | ||
| - Introduced standardized warning messages via new class `SPYWarning` | ||
| - Included (more or less) extensive developer docs | ||
| - Added Travis CI and included badges on GitHub landing page | ||
| - New convenience scripts to ease developing/testing | ||
| - New conda.yml file + script for consolidating conda/pip requirements: all | ||
| of SyNCoPy's dependencies are now collected in `syncopy.yml`, the respective | ||
| pip-specific requirements.txt and requirements-test.txt files are generated | ||
| on the fly by a new function `conda2pip` that relies on ruamel.yaml (new | ||
| required dependency for building SyNCoPy) | ||
| - New GitLab CI directive for uploading SyNCoPy to PyPI | ||
| - Included GitHub templates for new issues/pull requests | ||
| - SyNCoPy docu is now hosted on readthedocs (re-directed from syncopy.org) | ||
| - New logo + icon | ||
|
|
||
| ### CHANGED | ||
| - Made `cluster_cleanup` more robust (works with `LocalCluster` objects now) | ||
| - Made data-parser more feature-rich: check for emptiness, parse non-data | ||
| datasets etc. | ||
| - Made `generate_artificial_data` more robust: change usage of random number | ||
| seed to allow persistent comparisons across testing runs | ||
| - Updated CI dependencies (SyNCoPy now requires NumPy 1.18 and Matplotlib 3.3.x) | ||
|
|
||
| ### REMOVED | ||
| - All *.py-file headers have been removed | ||
| - Removed examples sub-module from main package (examples will be part of a | ||
| separate repo) | ||
|
|
||
| ### DEPRECATED | ||
| - Wiped all hand-crafted array-matching routines; use `best_match` instead | ||
| - Do not use `pbr` in the build system any more; rely instead on up-to-date | ||
| setuptools functionality | ||
| - Retired memory map support and raw binary data reading routines | ||
|
|
||
| ### FIXED | ||
| - Improved temporary storage handling so that dask workers that import the | ||
| package do not repeat all temp-dir I/O tests (and potentially run into | ||
| dead-locks or race conditions) | ||
|
|
||
| ## [v0.1a1] - 2019-10-14 | ||
| Preview alpha release of SyNCoPy for first ESI-internal tryout workshop. | ||
|
|
||
| ### NEW | ||
| - Added routines `esi_cluster_setup` and `cluster_cleanup` to facilitate | ||
| using SLURM from within SyNCoPy | ||
| - Included new `FauxTrial` class and `_preview_trial` class methods to | ||
| permit quick and performant compute dry-runs | ||
| - Included a `select` keyword to allow for in-place selections that are applied | ||
| on the fly in any meta-function via a new decorator. The heavy lifting is performed | ||
| by a new `Selector` class | ||
| - Re-worked the `specest` package: `mtmfft` is now fully functional | ||
| - Overhauled HTML documentation | ||
|
|
||
| ### CHANGED | ||
| - New layout of SyNCoPy objects on disk: introduction of Spy-containers supporting | ||
| multiple datasets/objects within the same folder | ||
| - First working implementation of `spy.load` and `spy.save` | ||
| - Use dask bags instead of arrays in parallelization engine to permit more | ||
| flexible distribution of data across workers | ||
| - Re-worked `trialdefinition` mechanics: attach the full `trialdefinition` array | ||
| to objects and fetch relevant information on the fly: `BaseData._trialdefinition` | ||
| unifies `sampleinfo`, `t0` and `trialinfo` and calls `definetrial` | ||
|
|
||
| ### REMOVED | ||
| - Removed `dimlabels` property | ||
|
|
||
| ### DEPRECATED | ||
| - Retired Dask arrays in `ComputationalRoutine`; use dask bags instead | ||
|
|
||
| ### FIXED | ||
| - Flipped sign of offsets in `trialdefinition` to be compatible w/FieldTrip | ||
| - Enforced PEP8 compliance | ||
| - Cleaned up constructor of `BaseData` to prohibit accessing uninitialized attributes | ||
|
|
||
| ## [v0.1a0] - 2019-07-20 | ||
| Internal pre-alpha release of SyNCoPy. Prototypes of data format, user-interface | ||
| and parallelization framework are in place. | ||
|
|
||
| ### NEW | ||
| - Class structure is laid out, meta-functions are present but mostly place-holders | ||
| - Support FieldTrip-style calling syntax via `cfg` "structures" (the keys of which are | ||
| "unwrapped" by a corresponding decorator) | ||
| - Preliminary I/O capabilities implemented, objects can be written/read | ||
| to/from HDF5 | ||
| - First prototype of parallelization framework based on Dask | ||
| - Custom traceback that is enabeld as soon as SyNCoPy is imported: do not | ||
| spill hundreds of lines to STDOUT, instead highlight most probable cause | ||
| of error and explain how to get to full traceback if wanted | ||
| - Basic session management to ensure concurrent SyNCoPy sessions only access | ||
| their own data |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,7 @@ | ||
| exclude .gitignore | ||
| exclude .gitlab-ci.yml | ||
| exclude .gitmodules | ||
| exclude MANIFEST.in | ||
| exclude .readthedocs.yml | ||
| exclude .travis.yml | ||
| recursive-exclude .github * | ||
| recursive-exclude doc * | ||
| recursive-include syncopy *.py |
Oops, something went wrong.