Changelog ========= 0.4.26 / 2023-06-08 ------------------- - ``NeuronCriteria`` now supports many new properties for the MANC v1.0 dataset. - Neuron property columns are determined from cached metadata rather than a full scan of the database. - If more than one ``Client`` has been constructed, none of them become automatically become the default client. In that case, you must explicitly pass a ``client`` argument to each query function you call. This avoids a common pitfall when dealing with multiple neuprint datasets (and therefore multiple Clients). - ``SynapseCriteria`` now uses a default confidence threshold based on the dataset metadata (instead of using 0.0 by default) - ``Client`` constructor avoids contacting the database unless it needs to. (Duplicate clients are now cheaper to construct.) - Minor enhancements to skeleton utilities, including a couple new analysis functions. - Added CITATION.cff 0.4.25 / 2022-09-15 ------------------- - In live-updated neuprint databases, it is possible that an edge's ``weight`` can become out-of-sync with its ``roiInfo`` totals. That inconsistency triggered an assertion in ``fetch_adjacencies()``, but now it will emit a warning instead. 0.4.24 / 2022-07-14 ------------------- - Implemented a workaround to avoid a pandas bug in certain cases involving empty dataframes. 0.4.23 / 2022-06-14 ------------------- - In ``fetch_adjacencies()`` (and ``fetch_simple_connections()``), we now ensure that no 0-weight "connections" are returned. .. note:: In recent neuprint databases, some ``:ConnectsTo`` relationships may have a ``weight`` of ``0``. In such cases, the relationship will have a non-zero ``weightHR`` (high-recall weight), but all of the relevant synapses are low-confidence, hence the "default" ``weight`` of ``0``. We now exclude such connections from our results. 0.4.22 / 2022-06-14 ------------------- - Fixed a crash that could occur if you supplied more than three regular expressions for ``type`` or ``instance``. - Fixed a problem involving 'hidden' ROIs in the hemibrain v1.0. 0.4.21 / 2022-05-14 ------------------- - Now ``heal_skeleton()`` is slightly faster in the case where no healing was necessary. 0.4.20 / 2022-05-13 ------------------- - By default, ``NeuronCriteria`` will now guess whether the ``type`` and ``instance`` contain a regular expression or not, so you don't need to explicitly pass ``regex=True``. Override the guess by specifying ``regex=True`` or ``regex=False``. 0.4.19 / 2022-05-12 ------------------- - Added ``fetch_mean_synapses()`` - Added ``attach_synapses_to_skeleton()`` 0.4.18 / 2022-04-06 ------------------- - Fixed broken package distribution. 0.4.17 / 2022-04-06 ------------------- - **[CHANGE IN RETURNED RESULTS]** ``fetch_synapse_connections()`` now applies ROI filtering criteria to only the post-synaptic points, for consistency with ``fetch_adjacencies()``. (See note in the docs.) This means that the number of synapses returned by ``fetch_synapse_connections()`` is now slightly different than it was in previous versions of ``neuprint-python``. - In ``fetch_neurons()``, better handling of old neuprint datasets which lack some fields (e.g. ``upstream``, ``downstream``, ``mito``). 0.4.16 / 2021-11-30 ------------------- - ``NeuronCriteria`` has new fields to support upcoming datasets: ``somaSide``, ``class_``, ``statusLabel``, ``hemilineage``, ``exitNerve``. - ``NeuronCriteria`` now permits you to search for neurons that contain (or lack) a particular property via a special value ``NotNull`` (or ``IsNull``). - ``fetch_neurons()`` now returns all neuron properties. - ``fetch_neurons()`` now returns special rows for NotPrimary connection counts. - The per-ROI connection counts table returned by ``fetch_neurons()`` now includes rows for connections which fall outside of all primary ROIs. These are indicated by the special ROI name ``NotPrimary``. - ``fetch_synapse_connections()`` uses a more fine-grained batching strategy, splitting the query across more requests to avoid timeouts. - Fixed a bug in ``fetch_shortest_paths()`` which caused it to generate invalid cypher if the ``intermediate_criteria`` used a list of bodyIds (or statuses, or rois, etc.) with more than three items. - ``fetch_output_completeness`` now accepts a list of statuses to use, rather than assuming only ``"Traced"`` neurons are complete. - Added utility function ``skeleton_segments()``. 0.4.15 / 2021-06-16 ------------------- - ``NeuronCriteria`` now accepts a boolean argument for ``soma``, indicating the presence or absence of a soma on the body. - Added ``fetch_connection_mitochondria()`` for finding the nearest mitochondria on both sides of a tbar/psd pair. (#24) - Integrated with Zenodo for DOI generation. 0.4.14 / 2021-03-27 ------------------- - Updated to changes in the neuPrint mitochondria data model. Older versions of ``neuprint-python`` cannot query for mitochondria any more. - ``fetch_neurons()``: Added new columns to the ``roi_counts_df`` result, for ``upstream, downstream, mito`` - ``fetch_skeletons()``: Now supports ``with_distances`` option - ``NeuronCriteria`` permits lists of strings for type/instance regular expressions. (Previously, lists were only permitted when ``regex=False``.) - Fixed a performance problem in ``fetch_synapse_connections()`` - More FAQ entries 0.4.13 / 2020-12-23 ------------------- - ``SynapseCriteria``: Changed the default value of ``primary_only`` to ``True``, since it may been counter-intuitive to obtain duplicate results by default. - ``NeuronCriteria``: Added ``cellBodyFiber`` parameter. (Philipp Shlegel #13) - Added mitochondria queries 0.4.12 / 2020-11-21 ------------------- - Better handling when adjacency queries return empty results - Simulation: Minor change to subprocess communication implementation - Skeleton DataFrames use economical dtypes - Minor bug fixes and performance enhancements - fetch_synapse_connections(): Fix pandas error in assertion 0.4.11 / 2020-06-30 ------------------- - Fixed ``ngspice`` install instructions. 0.4.10 / 2020-06-30 ------------------- - Moved skeleton-related functions into their own module, and added a few more skeleton utilty functions - Simulation: Support Windows - ``heal_skeleton():`` Allow caller to specify a maximum distance for repaired skeleton segments (#12) 0.4.9 / 2020-04-29 ------------------ - Added simulation functions and tutorial