Merge pull request #35 from 1313e/dev

Mark release of v1.2.3.

.azure-pipelines.yml

@@ -28,41 +28,51 @@ schedules:
 strategy:
   matrix:
     linux-python35:
-      imageName: 'ubuntu-16.04'
+      imageName: 'ubuntu-latest'
       python.version: '3.5'
     linux-python36:
-      imageName: 'ubuntu-16.04'
+      imageName: 'ubuntu-latest'
       python.version: '3.6'
     linux-python37:
-      imageName: 'ubuntu-16.04'
+      imageName: 'ubuntu-latest'
       python.version: '3.7'
+    linux-python38:
+      imageName: 'ubuntu-latest'
+      python.version: '3.8'
       upload_coverage: true
-    mac-python37:
-      imageName: 'macos-10.13'
-      python.version: '3.7'
+    mac-python38:
+      imageName: 'macOS-latest'
+      python.version: '3.8'
       upload_coverage: true
     windows-x86-python35:
-      imageName: 'windows-2019'
+      imageName: 'windows-latest'
       python.version: '3.5'
       python.arch: 'x86'
     windows-x86-python36:
-      imageName: 'windows-2019'
+      imageName: 'windows-latest'
       python.version: '3.6'
       python.arch: 'x86'
     windows-x86-python37:
-      imageName: 'windows-2019'
+      imageName: 'windows-latest'
       python.version: '3.7'
       python.arch: 'x86'
+    windows-x86-python38:
+      imageName: 'windows-latest'
+      python.version: '3.8'
+      python.arch: 'x86'
       upload_coverage: true
     windows-x64-python35:
-      imageName: 'windows-2019'
+      imageName: 'windows-latest'
       python.version: '3.5'
     windows-x64-python36:
-      imageName: 'windows-2019'
+      imageName: 'windows-latest'
       python.version: '3.6'
     windows-x64-python37:
-      imageName: 'windows-2019'
+      imageName: 'windows-latest'
       python.version: '3.7'
+    windows-x64-python38:
+      imageName: 'windows-latest'
+      python.version: '3.8'
       upload_coverage: true
       deploy: true
   maxParallel: 10
@@ -86,8 +96,14 @@ steps:
   displayName: Install missing libraries required for Qt on Linux
 
 # Install dependencies and PRISM
-- script: |
+- bash: |
     python -m pip install --upgrade pip setuptools wheel
+    if [[ $BUILD_SOURCEBRANCH == refs/heads/* ]] && [[ $BUILD_SOURCEBRANCH != "refs/heads/master" ]]; then
+      git clone -b dev https://github.com/1313e/e13Tools ../e13Tools
+      cd ../e13Tools
+      pip install .
+      cd -
+    fi
     pip install -r requirements_dev.txt
   displayName: Install testing dependencies
 

.codecov.yml

@@ -1,4 +1,6 @@
 codecov:
+    notify:
+        require_ci_to_pass: yes
     token: 6a194e41-c88d-4b7e-af10-29d9f54f8d84
 
 coverage:

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2019, Ellert van der Velden
+Copyright (c) 2019-2020, Ellert van der Velden
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -190,8 +190,8 @@ Huge thanks to James Josephides for making the *PRISM* logo.
 .. |Azure| image:: https://img.shields.io/azure-devops/build/1313e/2f7c67c7-61eb-4e70-9ff3-7f54f8e39987/1?logo=azure-pipelines&logoColor=white&label=Azure
     :target: https://dev.azure.com/1313e/PRISM/_build/latest?definitionId=1
     :alt: Azure Pipelines - Build Status
-.. |ReadTheDocs| image:: https://img.shields.io/readthedocs/e13tools/latest.svg?logo=read%20the%20docs&logoColor=white&label=Docs
-    :target: https://e13tools.readthedocs.io/en/latest
+.. |ReadTheDocs| image:: https://img.shields.io/readthedocs/prism-tool/latest.svg?logo=read%20the%20docs&logoColor=white&label=Docs
+    :target: https://prism-tool.readthedocs.io/en/latest
     :alt: ReadTheDocs - Build Status
 .. |Coverage| image:: https://img.shields.io/codecov/c/github/1313e/PRISM/master.svg?logo=codecov&logoColor=white&label=Coverage
     :target: https://codecov.io/gh/1313e/PRISM/branches/master

conftest.py

@@ -4,6 +4,7 @@
 # Package imports
 import matplotlib as mpl
 from py.path import local
+import _pytest
 import pytest
 
 
@@ -29,7 +30,8 @@ def pytest_configure(config):
 # This introduces a marker that auto-fails tests if a previous one failed
 def pytest_runtest_makereport(item, call):
     if "incremental" in item.keywords:
-        if call.excinfo is not None:
+        if(call.excinfo is not None and
+           call.excinfo.type is not _pytest.outcomes.Skipped):
             parent = item.parent
             parent._previousfailed = item
 

docs/source/api/prism.modellink.PolyLink.rst

@@ -0,0 +1,3 @@
+PolyLink
+========
+.. autoclass:: prism.modellink.PolyLink

docs/source/api/prism.modellink.rst

@@ -5,6 +5,7 @@ Classes
 .. toctree::
     prism.modellink.GaussianLink
     prism.modellink.ModelLink
+    prism.modellink.PolyLink
     prism.modellink.SineWaveLink
 
 Utilities

docs/source/community_guidelines.rst

@@ -8,30 +8,7 @@ Users are highly encouraged to make contributions to the package or request new
 If you would like to contribute to the package, but do not know what, then there are quite a few ToDos in the code that may give you some inspiration.
 As with contributions, if you find a problem or issue with *PRISM*, please do not hesitate to open a `GitHub issue`_ about it or post it on `Gitter`_.
 
-And, finally, if you use *PRISM* as part of your workflow in a scientific publication, please consider including an acknowledgement like *"Parts of the results in this work were derived using the PRISM Python package."* and citing the *PRISM* pipeline paper:
-
-.. code-block:: none
-    
-    @ARTICLE{2019ApJS..242...22V,
-        author = {{van der Velden}, E. and {Duffy}, A.~R. and {Croton}, D. and
-            {Mutch}, S.~J. and {Sinha}, M.},
-        title = "{Model dispersion with PRISM; an alternative to MCMC for rapid analysis of models}",
-        journal = {\apjs},
-        keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics},
-        year = "2019",
-        month = "Jun",
-        volume = {242},
-        number = {2},
-        eid = {22},
-        pages = {22},
-        doi = {10.3847/1538-4365/ab1f7d},
-        archivePrefix = {arXiv},
-        eprint = {1901.08725},
-        primaryClass = {astro-ph.IM},
-        adsurl = {http://adsabs.harvard.edu/abs/2019ApJS..242...22V},
-        adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-    }
-
+And, finally, if you use *PRISM* as part of your workflow in a scientific publication, please consider including an acknowledgement like *"Parts of the results in this work were derived using the PRISM Python package."* and citing the *PRISM* pipeline paper using the BibTeX-entry below.
 
 .. _GitHub issue: https://github.com/1313e/PRISM/issues
 .. _Gitter: https://gitter.im/1313e/PRISM
@@ -43,6 +20,34 @@ License
     :language: none
 
 
+Citation
+--------
+This BibTeX-entry is also available in *PRISM* using :func:`~prism._internal.get_bibtex` (available as :pycode:`prism.get_bibtex()`).
+
+.. code-block:: none
+    
+    @ARTICLE{2019ApJS..242...22V,
+       author = {{van der Velden}, Ellert and {Duffy}, Alan R. and {Croton}, Darren and
+         {Mutch}, Simon J. and {Sinha}, Manodeep},
+        title = "{Model Dispersion with PRISM: An Alternative to MCMC for Rapid Analysis of Models}",
+      journal = {\apjs},
+     keywords = {methods: data analysis, methods: numerical,
+        Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics},
+         year = 2019,
+        month = jun,
+       volume = {242},
+       number = {2},
+          eid = {22},
+        pages = {22},
+          doi = {10.3847/1538-4365/ab1f7d},
+archivePrefix = {arXiv},
+       eprint = {1901.08725},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2019ApJS..242...22V},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
 Additions
 ---------
 .. include:: additions.inc

docs/source/conf.py

@@ -22,7 +22,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PRISM'
-copyright = '2019, Ellert van der Velden'
+copyright = '2019-2020, Ellert van der Velden'
 author = 'Ellert van der Velden'
 
 # The short X.Y version

docs/source/user/hdf5.inc

@@ -42,6 +42,8 @@ An iteration data group (``'i'``) contains:
     - ``'emul_n'``: The data group that contains all data for a specific emulator system in this iteration.
       The value of ``'n'`` indicates which emulator system it is, not the data point.
       See below for its contents;
+    - ``'emul_space'``: The boundaries of the hypercube that encloses the parameter space in which this iteration is defined.
+      This is always equal to the plausible space of the previous iteration;
     - ``'impl_sam'``: The set of emulator evaluation samples that survived the implausibility checks and will be used to construct the next iteration;
     - ``'proj_hcube'``: The data group that contains all data for the (created) projections for this iteration, if at least one has been made. See below for its contents;
     - ``'sam_set'``: The set of model realization samples that were used to construct this iteration.
@@ -56,11 +58,12 @@ An iteration data group (``'i'``) contains:
 ----
 
 An emulator system data group (``'i/emul_n'``) contains:
-    - Attributes (5+): List the details about the model comparison data point used in this emulator system, including:
+    - Attributes (7+): List the details about the model comparison data point used in this emulator system, including:
 
         - Active parameters for this emulator system;
         - Data errors, identifiers, value space and value;
-        - Regression score and residual variance if regression was used.
+        - Regression score and residual variance if regression was used;
+        - The active and passive contributions to the residual variance (obtained from either the regression residual variance or the Gaussian sigma).
 
     - ``'cov_mat'``: The pre-calculated covariance matrix of all model evaluation samples in this emulator system.
       This data set is never used in *PRISM* and stored solely for user-convenience;
@@ -84,4 +87,5 @@ A projections data group (``'i/proj_hcube'``) contains individual projection dat
         - Projection depth and resolution.
 
     - ``'impl_los'``: The calculated line-of-sight depth for all grid points in this projection;
-    - ``'impl_min'``: The calculated minimum implausibility values for all grid points in this projection.
+    - ``'impl_min'``: The calculated minimum implausibility values for all grid points in this projection;
+    - ``'proj_space'``: The boundaries of the hypercube that encloses the defined parameter space of this projection.

docs/source/user/projections.inc

@@ -123,6 +123,11 @@ However, since the first value is still the highest implausibility value, that v
 Smoothing figures usually allows for 3D projections (2D projections rarely show this) to become less crowded, but they do throw away information.
 It should therefore only be used when necessary.
 
+.. versionadded:: 1.2.3
+    The `use_par_space` argument is also a bool, which controls whether the axes limits should be given by the model parameter space limits (:pycode:`True`) or by the parameter space over which the emulator iteration is defined (:pycode:`False`, default).
+    If :pycode:`False`, only the parameter space in which the emulator is defined is shown, which more often than not allows for more details to be seen in the projection figure.
+    If :pycode:`True`, the full model parameter space is used for the axes limits, allowing projection figures from different iterations to be compared with each other more easily.
+
 The `force` argument is a bool, which controls what to do if a projection is requested for which data already exists.
 If :pycode:`False` (default), it will use the previously acquired projection data to create the projection figure if it does not exist, skip if it does or return the figure data if `figure` is :pycode:`False`.
 If :pycode:`True`, the projection data and all associated projection figures will be deleted, and the projection will be recalculated.

prism/__init__.py

@@ -24,8 +24,7 @@
 
 # %% IMPORTS
 # Package imports
-from e13tools import compare_versions as _compare_versions
-from e13tools.utils import aux_char_set
+from e13tools import aux_char_set, compare_versions as _compare_versions
 from mpi4pyd import MPI as _MPI
 
 # PRISM imports

prism/__version__.py

@@ -10,7 +10,7 @@
 
 # %% VERSIONS
 # Default/Latest/Current version
-__version__ = '1.2.2'
+__version__ = '1.2.3'
 
 # Compatibility versions
 compat_version = ['1.0.0rc12']

prism/_docstrings.py

@@ -87,10 +87,11 @@
             Array containing the model outputs of all specified externally
             provided model evaluation samples."""
 ext_real_set_doc =\
-        """ext_real_set : list, dict or None{0}{1}
-            List of dicts containing an externally calculated set of model
-            evaluation samples and its data values, a dict with keys
-            ``['sam_set', 'mod_set']`` containing these dicts or *None* if no
+        """ext_real_set : str, list, dict or None{0}{1}
+            String indicating the suffix of the backup file that needs to be
+            used; list of dicts containing an externally calculated set of
+            model evaluation samples and its data values; a dict with keys
+            ``['sam_set', 'mod_set']`` containing these dicts; or *None* if no
             external set needs to be used."""
 ext_real_set_doc_s = ext_real_set_doc.format("", "")
 ext_real_set_doc_d = ext_real_set_doc.format(ds, "None")
@@ -255,24 +256,13 @@
 # %% PROJECTION DOCSTRINGS
 # Docstrings of draw_proj_fig methods
 draw_proj_fig_doc =\
-        """Draws the {0} projection figure for the provided `hcube`, given the
-        `impl_min` and `impl_los` values.
+        """Draws the {0} projection figure for the provided `hcube`.
 
         Parameters
         ----------
         hcube : 1D array_like of int of length {1}
             Array containing the internal integer identifiers of the main model
-            parameters that require a projection figure.
-        impl_min : 1D :obj:`~numpy.ndarray` object
-            List containing the lowest implausibility value that can be reached
-            in every single grid point on the given hypercube.
-        impl_los : 1D :obj:`~numpy.ndarray` object
-            List containing the fraction of the total amount of evaluated
-            samples in every single grid point on the given hypercube, that
-            still satisfied the implausibility cut-off criterion.
-        proj_res : int
-            Number of emulator evaluations used to generate the grid for the
-            given hypercube."""
+            parameters that require a projection figure."""
 
 # Description of hcube
 hcube_doc =\
@@ -436,6 +426,6 @@ class that was created for drawing *{0}*.
 save_data_doc_e = save_data_doc.format(
     std_emul_i_doc+"\n\t"+lemul_s_doc+"\n\t", "{'active_par'; "
     "'active_par_data'; 'cov_mat'; 'exp_dot_term'; 'mod_real_set'; "
-    "'regression'}")
+    "'regression', 'rsdl_var'}")
 save_data_doc_pr = save_data_doc.format(std_emul_i_doc+"\n\t",
                                         "{'nD_proj_hcube'}")

prism/_gui/core.py

@@ -13,7 +13,7 @@
 import signal
 
 # Package imports
-from e13tools.utils import docstring_append, raise_error
+import e13tools as e13
 import matplotlib as mpl
 from matplotlib.pyplot import switch_backend
 from qtpy import QtCore as QC, QtWidgets as QW
@@ -30,8 +30,8 @@
 
 # %% FUNCTION DEFINITIONS
 # This function starts up the Projection GUI 'Crystal'
-@docstring_append(start_gui_doc_pars, '\n\t\n\t')
-@docstring_append(start_gui_doc)
+@e13.docstring_append(start_gui_doc_pars, '\n\t\n\t')
+@e13.docstring_append(start_gui_doc)
 def start_gui(pipeline_obj):  # pragma: no cover
     # Create a logger
     logger = getCLogger('GUI')
@@ -44,7 +44,7 @@ def start_gui(pipeline_obj):  # pragma: no cover
     if not isinstance(pipeline_obj, Pipeline):
         err_msg = ("Input argument 'pipeline_obj' must be an instance of the "
                    "Pipeline class!")
-        raise_error(err_msg, TypeError, logger)
+        e13.raise_error(err_msg, TypeError, logger)
 
     # Activate worker mode
     with pipeline_obj.worker_mode:

prism/_gui/widgets/helpers.py

@@ -17,7 +17,7 @@
 from traceback import format_exception_only, format_tb
 
 # Package imports
-from e13tools.utils import docstring_substitute
+import e13tools as e13
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
 from qtpy import QtCore as QC, QtGui as QG, QtWidgets as QW
 
@@ -204,7 +204,7 @@ def create_traceback_box(self):
 
     # This function shows or hides the traceback box
     @QC.Slot()
-    @docstring_substitute(qt_slot=qt_slot_doc)
+    @e13.docstring_substitute(qt_slot=qt_slot_doc)
     def toggle_traceback_box(self):
         """
         Toggles the visibility of the traceback box and updates the dimensions
@@ -468,7 +468,7 @@ def open(self):
         self.thread.start()
 
         # While the thread is running, keep processing user input events
-        while self.thread.isAlive():
+        while self.thread.is_alive():
             qapp.processEvents()
             self.thread.join(0.1)
 
@@ -503,7 +503,7 @@ def raise_exception(self, exception):
 
     # This function kills all worker threads and then the controller thread
     @QC.Slot()
-    @docstring_substitute(qt_slot=qt_slot_doc)
+    @e13.docstring_substitute(qt_slot=qt_slot_doc)
     def kill_threads(self):
         """
         Terminates all currently running threads besides the main thread (on