pyOPALTools issueshttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues2019-07-20T15:49:58+02:00https://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/412d_halo_projection2019-07-20T15:49:58+02:00frey_m2d_halo_projectionfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/40Simplify interface2019-07-17T15:30:04+02:00frey_mSimplify interfacehttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/39Checking the usability of hvplot2019-07-07T16:47:52+02:00frey_mChecking the usability of hvplotWe might switch to [hvplot](https://hvplot.pyviz.org/) which is able to process different Python data frames.
CC: @adelmannWe might switch to [hvplot](https://hvplot.pyviz.org/) which is able to process different Python data frames.
CC: @adelmannhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/38Built ML database from sampler objectives2019-07-03T09:18:40+02:00frey_mBuilt ML database from sampler objectivesCurrently, we can only build ML databases from sampler output with stat-files. However, the sampler can write objectives to the JSON file like the optimizer.Currently, we can only build ML databases from sampler output with stat-files. However, the sampler can write objectives to the JSON file like the optimizer.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/37Use Dask for datasets2019-07-04T12:34:52+02:00frey_mUse Dask for datasetsWe should move from native `numpy` and `pandas` to `dask`. With `dask` we can run in parallel on large datasets.
https://dask.org/We should move from native `numpy` and `pandas` to `dask`. With `dask` we can run in parallel on large datasets.
https://dask.org/https://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/36Analyse Optimizer output2019-06-29T18:15:22+02:00frey_mAnalyse Optimizer outputSince https://gitlab.psi.ch/OPAL/src/merge_requests/102 OPAL writes a Pareto file. It would be nice having some tools to evaluate e.g. the *best* individual etc. A user might give function handles to be evaluated on the data set.Since https://gitlab.psi.ch/OPAL/src/merge_requests/102 OPAL writes a Pareto file. It would be nice having some tools to evaluate e.g. the *best* individual etc. A user might give function handles to be evaluated on the data set.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/35Optimizer: Pareto fron json file2019-06-24T09:55:38+02:00frey_mOptimizer: Pareto fron json fileThe optimizer data set is not able to handle the additional file.The optimizer data set is not able to handle the additional file.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/34Time attribute in h5 is not recognised2019-06-19T08:22:36+02:00adelmannTime attribute in h5 is not recognisedTime attribute in h5, created by a monitor is not recognisedTime attribute in h5, created by a monitor is not recognisedadelmannadelmannhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/33add_new_files_to_doc.sh presumes bash is located in /usr/bin/bash2019-06-17T15:35:33+02:00snuverink_jjochem.snuverink@psi.chadd_new_files_to_doc.sh presumes bash is located in /usr/bin/bashAs title says, which is not portable (at least not for SL6).
https://unix.stackexchange.com/questions/206350/what-is-the-difference-if-i-start-bash-with-bin-bash-or-usr-bin-env-bash proposes instead:
`#!/usr/bin/env bash`As title says, which is not portable (at least not for SL6).
https://unix.stackexchange.com/questions/206350/what-is-the-difference-if-i-start-bash-with-bin-bash-or-usr-bin-env-bash proposes instead:
`#!/usr/bin/env bash`snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/32Documentation style Sphinx2020-04-20T11:08:56+02:00frey_mDocumentation style Sphinx@bellotti\_r changed the documentation in some classes using [Sphinx](http://www.sphinx-doc.org/en/master/). It's similar to Doxygen. We should use a consistent format. I'm fine with the new proposed documentation.@bellotti\_r changed the documentation in some classes using [Sphinx](http://www.sphinx-doc.org/en/master/). It's similar to Doxygen. We should use a consistent format. I'm fine with the new proposed documentation.snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/31Field Output Files2020-06-03T08:56:13+02:00snuverink_jjochem.snuverink@psi.chField Output Files[Field output files](https://gitlab.psi.ch/OPAL/Manual-2.1/wikis/field-output) are not yet supported.[Field output files](https://gitlab.psi.ch/OPAL/Manual-2.1/wikis/field-output) are not yet supported.https://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/30Include mlmove branch into master2019-08-06T09:41:10+02:00frey_mInclude mlmove branch into master@ext\-neveu\_n Might it be possible to migrate the [mlmove](https://gitlab.psi.ch/OPAL/pyOPALTools/tree/mlmove) branch into the master?@ext\-neveu\_n Might it be possible to migrate the [mlmove](https://gitlab.psi.ch/OPAL/pyOPALTools/tree/mlmove) branch into the master?https://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/29ASCII Loss files2019-04-05T09:02:05+02:00snuverink_jjochem.snuverink@psi.chASCII Loss filesRequested by @ext\-calvo\_p : loss files (.loss) are missing.Requested by @ext\-calvo\_p : loss files (.loss) are missing.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/28Clean up timing directory2019-04-06T15:27:01+02:00frey_mClean up timing directoryfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/27Remove deprecated amrPlots directory.2019-04-06T15:27:01+02:00frey_mRemove deprecated amrPlots directory.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/26Removing of deprecated profiling directory2019-04-06T15:27:01+02:00frey_mRemoving of deprecated profiling directoryThe plots in *profiling/Memory.py* and *profiling/LoadBalancing.py* are already covered in the new opal package.The plots in *profiling/Memory.py* and *profiling/LoadBalancing.py* are already covered in the new opal package.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/25Removing deprecated pyH5root2019-04-06T15:27:01+02:00frey_mRemoving deprecated pyH5rootfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/24Switching between plotting styles does not work properly2019-04-01T15:39:50+02:00frey_mSwitching between plotting styles does not work properlyWhen calling for example the ```jupyter``` style and then the ```poster``` style, the ```matplotlib.rcParams``` are not all set.When calling for example the ```jupyter``` style and then the ```poster``` style, the ```matplotlib.rcParams``` are not all set.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/23Classes for dat a computation2019-04-06T15:27:01+02:00frey_mClasses for dat a computationAs done in #22 we should do the same for data computations.As done in #22 we should do the same for data computations.frey_mfrey_mhttps://gitlab.psi.ch/OPAL/pyOPALTools/-/issues/22Plotting Classes2019-04-06T15:27:01+02:00frey_mPlotting ClassesAs discussed with @gsell we should implement base classes for plotting in order to avoid the if-statements
```Python
if not isinstance(ds, DatasetBase):
raise TypeError("Dataset '" + ds.filename +
"' not d...As discussed with @gsell we should implement base classes for plotting in order to avoid the if-statements
```Python
if not isinstance(ds, DatasetBase):
raise TypeError("Dataset '" + ds.filename +
"' not derived from 'DatasetBase'.")
if not ds.filetype == FileType.OPTIMIZER:
raise TypeError(ds.filename + ' is not an optimizer dataset.')
```
Each dataset would also be derived from the appropriate plotter class. This would also simplify adding new methods and avoiding errors.frey_mfrey_m