Llnl-hatchet

Version `2022.2.0` is a major release.

* Adds writers module to installed modules to resolve package install
* CaliperReader bug fixes: filter records to parse, ignore function metadata
field
* Modify graphframe copy/deepcopy
* Adds beautiful soup 4 to requirements.txt
* Add new page on using hatchet on LLNL systems

This is a minor release on the `2022.1` series. It addresses a bug fix in
Hatchet's query language and Hatchet's flamegraph output:

* flamegraph: change count to be an int instead of a float
* query language: fix edge cases with + wildcard/quantifier by replacing it
with `.` followed by `*`

Version `2022.1.0` is a major release.

New features
* 3 new readers: TAU, SpotDB, and Caliper python reader
* Query language extensions: compound queries, not query, and middle-level API
* Adds GraphFrame checkpoints in HDF5 format
* Interactive CCT visualization enhancements: pan and zoom, module encoding,
multivariate encoding and adjustable mass pruning on large datasets
* HPCToolkit: extend for GPU stream data
* New color maps for terminal tree visualization
* New function for calculating exclusive metrics from corresponding inclusive
metrics

Changes to existing APIs
* Precision parameter applied to second metric in terminal tree visualization
(e.g., `gf.tree(precision=3)`)
* Deprecates `from_caliper_json()`, augments existing `from_caliper()` to
accept optional cali-query parameter and cali file or just a json file
* Metadata now stored on the GraphFrame
* New interface for calling the Hatchet calling context tree from Roundtrip:
`%cct <graphframe or list>`. Deprecated interface: `%loadVisualization
<roundtrip_path> <literal_tree>`
* Add recursion limit parameter to graphframe filter(rec_limit=1000)`,
resolving recursion depth errors on large graphs

Tutorials and documentation
* New tutorial material from the ECP Annual Meeting 2021
* New developer and contributor guides
* Added section on how to generate datasets for Hatchet and expanded
* documentation on the query language

Internal updates
* Extend update_inclusive_columns() for multi-indexed trees
* Moves CI from Travis to GitHub Actions
* Roundtrip refactor
* New unit test for formatting license headers

Bugfixes
* Return default_metric and metadata in filter(), squash(), copy(), and
deepcopy()
* flamegraph: extract name from dataframe column instead of frame
* Preserve existing inc_metrics in update_inclusive_columns

This release extends the query language to support querying nodes that
fall within a range and includes a critical fix for using the query language on
a dataframe that may contain nan and infs values.

New features
* Timemory reader
* Query dataframe columns with GraphFrame.show_metric_columns()
* Query nodes within a range using the call path query language
* Extend readers to define their own default metric

Changes to existing APIs
* Tree visualization displays 2 metrics
* Literal output format: add hatchet node IDs
* Parallel implementationo of filter function
* Caliper reader: support multiple hierarchies in JSON format
* Adds multiprocessing dependency

Bugfixes
* Improve querying of subtrees in interactive visualization
* Tree visualization: check for both nan and inf
* Query language: match nodes with nan and inf values
* Check for exclusive metrics before updating inclusive columns

This release introduces a new tree visualization for Jupyter to interact with
the data, deprecates some of the tree parameters, adds cython as a dependency,
and contains performance improvements to two of Hatchet's central APIs.

New features

* Interactive tree visualization in Jupyter
* Add mult and division API
* Update hatchet installation steps for cython integration
* Readers: cprofiler, pyinstrument
* Graph output formats: to_literal
* Add profiling APIs to profile Hatchet APIs
* Update basic tutorial for hatchet

Changes to existing APIs

* Remove threshold=, color=, and unicode= from tree API
* Highlighting name disabled by default in terminal tree output
is kept in sync with the dataframe
* Internal performance improvements to unify and HPCToolkit reader, enabling
analysis of large datasets
* For mathematical operations, insert nan values for missing nodes, show values
as nan and inf as necessary in dataframe
* Extend callpath query language to support non-dataframe metrics (e.g., depth,
hatchet ID)
* Literal reader: A node can be defined with a "duplicate": True field if it
should be the same node (though in a different callpath). A node also needs
"frame" field, which is a dict containing the node "name" and "type" (if
necessary).

Bugfixes

* caliper reader: do not assume "path" column is present, create graph after
reading metadata
* fix updating inclusive columns for multi-indexed dataframes (required as part
of squash)
* fix unicode error in python2 for terminal-based tree output

This release adds a syntax query language as an alternative method for
filtering the graph. It also refreshes the tree printout with an updated
format and legend.

New features

* Add graph syntax query language to filter the graph
* Update HPCToolkit reader to handle sec or usec time units

Changes to existing APIs

* Add squash parameter to filter function to perform filter and squash in a
single call
* Filter function takes an object, which can be a user-supplied function or a
query object
* Tree printout format updated
* Tree printout API parameter changes:
- Removed parameters: ``color`` deprecated (color determined based on terminal support),
``threshold``, and ``unicode``
- Changed parameters: ``metric`` changed to ``metric_column``, ``name`` changed to
``name_column``, ``invert_colors`` changed to ``invert_colormap``,
``expand_names`` changed to ``expand_name``, and ``context`` changed to
``context_column``
- added ``highlight_name`` to highlight user code (from non-user code)

Bugfixes

* Sort nodes in union and tree printout by their frame
* Fix squash edge case where multiple parents are the same