Flopy

* New features:

* [feat(ModflowAg)](https://github.com/modflowpy/flopy/commit/c89b2d83a81125c986c05df57ffc980fe10fd663): Add the modflowag package for nwt (pull request #922). Committed by Joshua Larsen on 2020-06-25.
* [feat(GridIntersect)](https://github.com/modflowpy/flopy/commit/176c9b45eb158217b1aeb0657d60ed06739e53e6): #902 (903). Committed by Davíd Brakenhoff on 2020-06-10.
* [feat(mbase)](https://github.com/modflowpy/flopy/commit/4fc61d573c108be7601a2e8479a86c35040998c2): Suppress duplicate package warning if verbose is false (#908). Committed by Hughes, J.D on 2020-06-09.
* [feat(ModflowSms)](https://github.com/modflowpy/flopy/commit/f539d072e20cb5654fab8826ac3bbaf7d1f8b52e): Add support for simple, moderate, complex (#906). Committed by langevin-usgs on 2020-06-09.
* [feat(str)](https://github.com/modflowpy/flopy/commit/3182f57479c1a45d614151867f419a0d35f7f2c2): Add irdflg and iptflg control to str (#905). Committed by Hughes, J.D on 2020-06-09.
* [feat(Mf6ListBudget)](https://github.com/modflowpy/flopy/commit/04b74bd8fb4ed71cf0ed07f721204296b9fd4388): Add support for mf6 budgets with multiple packages with same name (#900). Committed by langevin-usgs on 2020-06-02.
* [feat(mfchd.py)](https://github.com/modflowpy/flopy/commit/88fbd4ccdf837dd4b2a70795522fcaa0a2470dfe): Prevent write chk-file always (#869). Committed by Ralf Junghanns on 2020-05-08.
* [feat(set all data external)](https://github.com/modflowpy/flopy/commit/0336b5c4f6c62994a7ffea26318240fbaa0ca1fb): Set all data external for simulation (#846). Committed by spaulins-usgs on 2020-04-08.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/e43dccc29d87e182aaa82687968d98391fa78e5d): Improve export at vertices (#844). Committed by Etienne Bresciani on 2020-04-06.
* [feat(netcdf)](https://github.com/modflowpy/flopy/commit/fb942b4675c335247b81f9287bdb8cdb3bcf360b): Use modern features from pyproj>=2.2.0 (#840). Committed by Mike Taves on 2020-03-31.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/b975368a9c5a25df616b024a08450056e92b6426): Export vectors to vtk. Committed by Etienne Bresciani on 2020-03-31.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/13c1dd28b9c470c70aac624b70888f5f6badf795): Export in .vti and .vtr when possible. Committed by Etienne Bresciani on 2020-03-28.
* [feat(vectors)](https://github.com/modflowpy/flopy/commit/1284871e5b8ed26c9d925e28295c2098a76b1bc9): Vector plots when stresses applied along boundaries (#817). Committed by langevin-usgs on 2020-03-05.
* [feat(plot_bc)](https://github.com/modflowpy/flopy/commit/207cd1ee5dde116e5b8912232d9b94a9c9304161): Updated plot_bc for maw, uzf, sfr, and multiple bc packages (#808). Committed by Joshua Larsen on 2020-02-11.
* [feat(disl grids)](https://github.com/modflowpy/flopy/commit/469727bcb695ee42611f3df227830ef3b25853f6): Support for 1d vertex grids. fix for writing gridlines to shapefile (#799). Committed by spaulins-usgs on 2020-02-04.
* [feat(zb netcdf)](https://github.com/modflowpy/flopy/commit/491f4fe3923a942e9a0d535a7da54173c4df1204): Zonebudget netcdf export support added (#781). Committed by Joshua Larsen on 2020-01-17.
* [feat(mf6 checker)](https://github.com/modflowpy/flopy/commit/088f147f1d761875f3a1ffabdda82312c002305a): Input data check for mf6 (#779). Committed by spaulins-usgs on 2020-01-16.


* Bug fixes:

* [fix(280, 835)](https://github.com/modflowpy/flopy/commit/6dae1b0ed5df6836ce6ea981de7050621a90477f): Set_all_data_external now includes constants, cellids in list data are checked (#920). Committed by spaulins-usgs on 2020-06-23.
* [fix(mfsfr2.check)](https://github.com/modflowpy/flopy/commit/796b7b15385de0181cabd33d3bc1915bfa76a83b): Negative segments for lakes no longer included in segment numbering order check (#915). Committed by aleaf on 2020-06-23.
* [fix(GridIntersect)](https://github.com/modflowpy/flopy/commit/d5672f585faa31ead48973834d9b30cf70512cba): Fixes #916 and 917 (918). Committed by Davíd Brakenhoff on 2020-06-22.
* [fix(ZoneBudget)](https://github.com/modflowpy/flopy/commit/0207372769c5389835c555820c11fc377a4370c7): Fix faulty logic in ZoneBudget (#911). Committed by Jason Bellino on 2020-06-22.
* [fix(SwtListBudget)](https://github.com/modflowpy/flopy/commit/eed5afdd03917256b097a797ec1137c2b80fb8a1): Totim was not being read correctly for seawat list file (#910). Committed by langevin-usgs on 2020-06-10.
* [fix(Seawat.modelgrid)](https://github.com/modflowpy/flopy/commit/7a31a1d7a210894d9970e2e7a3a6a6453518289b): Pass lenuni from dis file into modelgrid instance (#901). Committed by Joshua Larsen on 2020-06-02.
* [fix(mfsimulation)](https://github.com/modflowpy/flopy/commit/0958b28added4b572b168c35657f1d5fd968e952): Repair change for case insensitive model names (#897). Committed by langevin-usgs on 2020-06-01.
* [fix(_plot_util3d_helper, export_array)](https://github.com/modflowpy/flopy/commit/617b98dd0f5750c7cf4d1a9e8376e00fdb4e94bf): (#895). Committed by Joshua Larsen on 2020-06-01.
* [fix()](https://github.com/modflowpy/flopy/commit/8e70c9284490b220ef6fe759b0fafbb5d252f1ae): fix building in clean env (#894). Committed by Ritchie Vink on 2020-05-28.
* [fix(setup.py)](https://github.com/modflowpy/flopy/commit/b80a89c18821fe1bc7375c15e4c03d1e0be70916): Read package name, version, etc. from version.py (#893). Committed by Hughes, J.D on 2020-05-26.
* [fix(MFSimulation)](https://github.com/modflowpy/flopy/commit/3cec7929f323e7753ef80e95b31a64a6105dce41): Remove case sensitivity from register_ims_package() (#890). Committed by Joshua Larsen on 2020-05-25.
* [fix(modelgrid)](https://github.com/modflowpy/flopy/commit/bb861ac2f05e7e8d38a832d03ae0a45a2249d10d): Fix offset for xul and yul in read_usgs_model_reference_file and attribs_from_namfile_header (#889). Committed by Joshua Larsen on 2020-05-19.
* [fix(886)](https://github.com/modflowpy/flopy/commit/f4e5ed39c5316e9bd2b7941c31f1b91253cd51e5): Mfarray aux variable now always returned as an numpy.ndarray. fixed problem with pylistutil not fully supporting numpy.ndarray type. (#887). Committed by spaulins-usgs on 2020-05-19.
* [fix(CellBudgetFile)](https://github.com/modflowpy/flopy/commit/29d7f849f8d2f160a537494661bd096a9e1c1253): Update for auto precision with imeth = 5 or 6 (#876). Committed by Joshua Larsen on 2020-05-14.
* [fix(870)](https://github.com/modflowpy/flopy/commit/cbf1f65a8f3389f55bb55249ce8c358ac06cf75c): Update ims name file record after removing ims package (#880). Committed by Joshua Larsen on 2020-05-14.
* [fix](https://github.com/modflowpy/flopy/commit/e3a6c26fe8ad39c69cd5fec78064f12d2edbb521): #868, 874, 879 (881). Committed by spaulins-usgs on 2020-05-14.
* [fix(867)](https://github.com/modflowpy/flopy/commit/265fc7c64956b9165b9be2607680de086a9cf973): Fixed minimum record entry count for lists to never include keywords in the count (#875). Committed by spaulins-usgs on 2020-05-11.
* [fix(SfrFile)](https://github.com/modflowpy/flopy/commit/4100de2b80cdb542e820f3b41a88eaf9865fa63d): Update sfrfile for streambed elevation when present (#866). Committed by Joshua Larsen on 2020-05-04.
* [fix(831,858)](https://github.com/modflowpy/flopy/commit/a177d59c691367e568de07b340d53e8b1f2322fb): Data length check and case-insensitive lookup (#864). Committed by spaulins-usgs on 2020-05-01.
* [fix(856)](https://github.com/modflowpy/flopy/commit/c45a5e5f1fb2f8224d87307564b68dc1c30063d9): Specifying period data with value none now only removes data from that period. also, fixed an unrelated problem by updating the multi-package list. (#857). Committed by spaulins-usgs on 2020-04-22.
* [fix(plot_array)](https://github.com/modflowpy/flopy/commit/f6545ff28004f4f6573e07aab939d774230df0a6): Update plot_array method to mask using np.ma.masked_values (#851). Committed by Joshua Larsen on 2020-04-15.
* [fix(ModflowDis)](https://github.com/modflowpy/flopy/commit/52ecd98a11fc4f459c9bd0b59cb854ff402eeb08): Zero based get_node() and get_lrc()… (#847). Committed by Joshua Larsen on 2020-04-10.
* [fix(binaryfile_utils, CellbudgetFile)](https://github.com/modflowpy/flopy/commit/f514a22a38264dc81c0db6dae62db4beae8df227): Update for imeth == 6 (#823). Committed by Joshua Larsen on 2020-04-10.
* [fix(utils.gridintersect)](https://github.com/modflowpy/flopy/commit/14040ff605dfe496d8ec88ca8eeb3f73daeee06e): Bug in gridintersect for vertex grids (#845). Committed by Davíd Brakenhoff on 2020-04-06.
* [fix(mflmt.py)](https://github.com/modflowpy/flopy/commit/1f322f0ef50be9dfaa2252cacb091aded4159113): Clean up docstring for package_flows argument in lmt. Committed by emorway-usgs on 2020-03-31.
* [fix(str)](https://github.com/modflowpy/flopy/commit/59cac5c0466b497c36e833784b436d4a5e47fcd5): Add consistent fixed and free format approach (#838). Committed by Hughes, J.D on 2020-03-31.
* [fix(vtk)](https://github.com/modflowpy/flopy/commit/aa9f3148008dd4c23d86db4e4dae5bae8c8bc564): Issues related to nan and type cast. Committed by Etienne Bresciani on 2020-03-31.
* [fix(pyproj)](https://github.com/modflowpy/flopy/commit/9a1b9e344aefad4ed222bd8d10eb6b9000c9c7d0): Pyproj.proj's errcheck keyword option not reliable (#837). Committed by Mike Taves on 2020-03-29.
* [fix](https://github.com/modflowpy/flopy/commit/4bfab916592784180d57df59b78d190e28c9099b): (#830): handling 'none' cellids in sfr package (834). Committed by spaulins-usgs on 2020-03-25.
* [fix()](https://github.com/modflowpy/flopy/commit/90a498ea2356e0eca7ddbf1c89a0f5f12f14b5a3): Fix quasi3d plotting (#819). Committed by Ruben Caljé on 2020-03-02.
* [fix(ModflowSfr2.export)](https://github.com/modflowpy/flopy/commit/b6c9a3a6668ee8a35fda785da3709bd4842b7ba9): Update modflowsfr2.export() to use grid instead of spatialreference (#820). Committed by Joshua Larsen on 2020-02-28.
* [fix(flopy3_MT3DMS_examples.ipynb)](https://github.com/modflowpy/flopy/commit/65e8adaeea55a14a3d61c125801741c5b9ceb699): Wrong indices were indexed (#815). Committed by Eric Morway on 2020-02-20.
* [fix(build_exes.py)](https://github.com/modflowpy/flopy/commit/f3136a233274baa63ace7555d862c43bc67894f5): Fix bugs for windows (#810) (813). Committed by Etienne Bresciani on 2020-02-18.
* [fix(mflist)](https://github.com/modflowpy/flopy/commit/4a885a107ee5ead5a116f95bb1f7f60549cba295): Default value not working (#812). Committed by langevin-usgs on 2020-02-13.
* [fix(flopy3_MT3DMS_examples.ipynb)](https://github.com/modflowpy/flopy/commit/0d152513d4ecb84fd474cb0495dd0676f05d5b72): Match constant heads to original problem (#809). Committed by Eric Morway on 2020-02-11.
* [fix(vtk)](https://github.com/modflowpy/flopy/commit/ab8120bc3dc1214fef90077ade226471900b89d5): Change in export_cbc output file name (#795). Committed by rodrperezi on 2020-01-30.
* [fix(mf6)](https://github.com/modflowpy/flopy/commit/84ee8a72b00fbcd8e7f396af9b356170634cfda6): Update create packages to support additional models (#790). Committed by Hughes, J.D on 2020-01-24.
* [fix(remove_package)](https://github.com/modflowpy/flopy/commit/102d25b23dc0281cccf65eb0a9d3cc8b05755484): Fixed remove_package to rebuild namefile recarray correctly after removing package - issue #776 (784). Committed by spaulins-usgs on 2020-01-17.
* [fix(gridgen)](https://github.com/modflowpy/flopy/commit/061c72771ae4bc023e970bf9048a4c53bba2ba80): X, y center was not correct for rotated grids (#783). Committed by langevin-usgs on 2020-01-16.
* [fix(mtssm.py)](https://github.com/modflowpy/flopy/commit/f7886e2762464f69ae6b1e3ef1124bbee017b8a8): Handle 1st stress period with incrch equal to -1 (#780). Committed by Eric Morway on 2020-01-16.
* [fix(vtk)](https://github.com/modflowpy/flopy/commit/73f70518238ff383628ba25066c41647e875dc2e): Change in export_model when packages_names is none (#770). Committed by rodrperezi on 2019-12-30.
* [fix()](https://github.com/modflowpy/flopy/commit/ec71e6ce2d2f4bc3d05e3172cccba6c42bf26b87): fix(repeating blocks) (#771). Committed by spaulins-usgs on 2019-12-30.
* [fix(replace package)](https://github.com/modflowpy/flopy/commit/cf3586f0602acd20c9c672b2c763f09c6a252e00): When a second package of the same type is added to a model, the model now checks to see if the package type supports multiple packages. if it does not it automatically removes the first package before adding the second (#767). (768). Committed by spaulins-usgs on 2019-12-18.
* [fix(Mflist)](https://github.com/modflowpy/flopy/commit/51d80641e81f844490306d2cddefacb21bda8302): Allow none as a list entry (#765). Committed by langevin-usgs on 2019-12-16.

* **Dropped support for python 2.7**
* Switched from [pangeo binder](https://aws-uswest2-binder.pangeo.io/) binder to [mybinder.org binder](https://mybinder.org)
* Added support for MODFLOW 6 Skeletal Compaction and Subsidence (CSUB) package

* Bug fixes:

* Fix issue in MNW2 when the input file had spaced between lines in Dataset 2. [736](https://github.com/modflowpy/flopy/pull/736)
* Fix issue in MNW2 when the input file uses wellids with inconsistent cases in Dataset 2 and 4. Internally the MNW2 will convert all wellids to lower case strings. [736](https://github.com/modflowpy/flopy/pull/736)
* Fix issue with VertexGrid plotting errors, squeeze proper dimension for head output, in `PlotMapView` and `PlotCrossSection`
* Fix issue in `PlotUtilities._plot_array_helper` mask MODFLOW-6 no flow and dry cells before plotting
* Removed assumption that transient SSM data appears in the first stress period [754](https://github.com/modflowpy/flopy/issues/754) [#756](https://github.com/modflowpy/flopy/issues/754). Fix includes a new autotest ([t068_test_ssm.py](https://github.com/modflowpy/flopy/blob/develop/autotest/t068_test_ssm.py)) that adds transient concentration data after the first stress period.
* Fix issues with add_record method for MfList [758](https://github.com/modflowpy/flopy/pull/758)

**<span style="color:red" style="text-decoration:underline">Support for Python versions < 3.5 will be dropped in the next version of FloPy (version 3.3.0)</span>**

* ModflowFlwob: Variable `irefsp` is now a zero-based integer ([596](https://github.com/modflowpy/flopy/pull/596))
* ModflowFlwob: Added a load method and increased precision of `toffset` when writing to file ([598](https://github.com/modflowpy/flopy/pull/598))
* New feature GridIntersect ([610](https://github.com/modflowpy/flopy/pull/610)): The GridIntersect object allows the user to intersect shapes (Points, LineStrings and Polygons) with a MODFLOW grid. These intersections return a numpy.recarray containing the intersection information, i.e. cell IDs, lengths or areas, and a shapely representation of the intersection results. Grids can be structured or vertex grids. Two intersections methods are implemented: `"structured"` and `"strtree"`: the former accelerates intersections with structured grids. The latter is more flexible and also works for vertex grids. The GridIntersect class is available through `flopy.utils.gridintersect`. The functionality requires the Shapely module. See the [example notebook](../examples/Notebooks/flopy3_grid_intersection_demo.ipynb) for an overview of this new feature.
* New feature `Raster` ([634](https://github.com/modflowpy/flopy/pull/634)): The Raster object allows the user to load raster files (Geotiff, arc ascii, .img) and sample points, sample polygons, create cross sections, crop, and resample raster data to a Grid. Cropping has been implemented using a modified version of the ray casting algorithm for speed purposes. Resampling a raster can be performed with structured, vertex, and unstructured Grids. Rasters will return a numpy array of resampled data in the same shape as the Grid. The Raster class is available by calling `flopy.utils.Raster`. The functionality requires rasterio, affine, and scipy. See the ([example notebook](../examples/Notebooks/flopy3_raster_intersection.ipynb)) for an overview of this feature.
* Modify NAM and MFList output files to remove excessive whitespace ([622](https://github.com/modflowpy/flopy/pull/622), [#722](https://github.com/modflowpy/flopy/pull/722))
* Deprecate `crs` class from `flopy.utils.reference` in favor of `CRS` class from `flopy.export.shapefile_utils` ([608](https://github.com/modflowpy/flopy/pull/608))
* New feature in `PlotCrossSection` ([660](https://github.com/modflowpy/flopy/issues/660)). Added a `geographic_coords` parameter flag to `PlotCrossSection` which allows the user to plot cross sections with geographic coordinates on the x-axis. The default behavior is to plot distance along cross sectional line on the x-axis. See the ([example notebook](../examples/Notebooks/flopy3_PlotCrossSection_demo.ipynb)) for an overview of this feature.
* New feature with binaryfile readers, including `HeadFile` and `CellBudgetFile` ([669](https://github.com/modflowpy/flopy/pull/669)): [`with` statement](https://docs.python.org/3/reference/compound_stmts.html#with) is supported to open files for reading in a context manager, which automatically close when done or if an exception is raised.
* Improved the flopy list reader for MODFLOW stress packages (for mf2005, mfnwt, etc.), which may use SFAC to scale certain columns depending on the package. The list reading now supports reading from external files, in addition to open/close. The (binary) option is also supported for both open/close and external. This new list reader is used for reading standard stress package lists and also lists used to create parameters. The new list reader should be consistent with MODFLOW behavior.
* SfrFile detects additional columns ([708](https://github.com/modflowpy/flopy/issues/708))
* Add a `default_float_format` property to mfsfr2, which is string formatted by NumPy versions > 1.14.0, or `{:.8g}` for older NumPy versions ([710](https://github.com/modflowpy/flopy/issues/710))
* Support for pyshp 1.2.1 dropped, pyshp 2.1.0 support maintained
* Improved VTK export capabilities. Added export for VTK at array level, package level, and model level. Added binary head file export and cell by cell file export. Added the ability to export point scalars in addition to cell scalars, and added smooth surface generation. VTK export now supports writing transient data as well as exporting to binary .vtu files.
* Support for copying model and package instances with `copy.deepcopy()`
* Added link to Binder on [README](README.md) and [notebooks_examples](../examples/docs/notebook_examples.md) markdown documents. Binder provides an environment that runs and interactively serves the FloPy Jupyter notebooks.

* Bug fixes:

* When using the default `iuzfbnd=None` in the `__init__` routine of mtuzt.py, instantiation of IUZBND was generating a 3D array instead of a 2D array. Now generates a 2D array
* ModflowSfr2 `__init__` was being slowed considerably by the `ModflowSfr2.all_segments` property method. Modified the `ModflowSfr2.graph` property method that describes routing connections between segments to handle cases where segments aren't listed in stress period 0.
* Ensure disordered fields in `reach_data` (Dataset 2) can be supported in `ModflowSfr2` and written to MODFLOW SFR input files.
* When loading a MF model with UZF active, item 8 ("`[IUZROW]` `[IUZCOL]` `IFTUNIT` `[IUZOPT]`") wasn't processed correctly when a user comment appeared at the end of the line
* MODFLOW-6 DISU JA arrays are now treated as zero-based cell IDs. JA, IHC, CL12 are outputted as jagged arrays.
* Models with multiple MODFLOW-6 WEL packages now load and save correctly.
* Exporting individual array and list data to a shapefile was producing an invalid attribute error. Attribute reference has been fixed.
* Fix UnboundLocalError and typo with `flopy.export.shapefile_utils.CRS` class ([608](https://github.com/modflowpy/flopy/pull/608))
* Fix Python 2.7 issue with `flopy.export.utils.export_contourf` ([625](https://github.com/modflowpy/flopy/pull/625))
* When loading a MT3D-USGS model, keyword options (if used) were ignored ([649](https://github.com/modflowpy/flopy/pull/649))
* When loading a modflow model, spatial reference information was not being passed to the SpatialReference class ([659](https://github.com/modflowpy/flopy/issues/659))
* Fix specifysurfk option in UZF, ModflowUZF1 read and write surfk variable
* Fix minor errors in flopy gridgen wrapper
* Close opened files after loading, to reduce `ResourceWarning` messages ([673](https://github.com/modflowpy/flopy/issues/673))
* Fix bugs related to flake8's F821 "undefined name 'name'", which includes issues related to Mt3dPhc, ModflowSfr2, ModflowDe4, ListBudget, and ModflowSms ([686](https://github.com/modflowpy/flopy/issues/686))
* Fix bugs related to flake8's F811 "redefinition of unused 'name'" ([688](https://github.com/modflowpy/flopy/issues/688))
* Fix bugs related to flake8's W605 "invalid escape sequence '\s'" (or similar) ([700](https://github.com/modflowpy/flopy/issues/700))
* Fix EpsgReference class behavior with JSON user files ([702](https://github.com/modflowpy/flopy/issues/702))
* Fix ModflowSfr2 read write logic for all combinations of isfropt and icalc
* IRCH array of the Recharge Package is now a zero-based variable, which means an IRCH value of 0 corresponds to the top model layer ([715](https://github.com/modflowpy/flopy/issues/715))
* MODFLOW lists were not always read correctly if they used the SFAC or binary options or were used to define parameters ([683](https://github.com/modflowpy/flopy/issues/683))
* Changed VDF Package density limiter defaults to zero ([646](https://github.com/modflowpy/flopy/issues/646))

* Added a check method for OC package (558)
* Change default map projection from EPSG:4326 to None (535)
* Refactor warning message visibility and categories (554, 575)
* Support for MODFLOW 6 external binary files added. Flopy can read/write binary files containing list and array data (470, 553).
* Added silent option for MODFLOW 6 write_simulation (552)
* Refactored MODFLOW-6 data classes. File writing operations moved from mfdata*.py to new classes created in mffileaccess.py. Data storage classes moved from mfdata.py to mfdatastorage.py. MFArray, MFList, and MFScalar interface classes simplified with most of the data processing code moved to mfdatastorage.py and mffileaccess.py.
* Added MODFLOW 6 quickstart example to front page.
* Added lgrutil test as autotest/t063_test_lgrutil.py and implemented a get_replicated_parent_array() method to the Lgr class so that the user can pass in a parent array and get back an array that is the size of the child model.
* Refactored much of the flopy code style to conform with Python conventions and those checked by Codacy. Added an automated Codacy check as part of the pull request and commit checks.

* Bug fixes:

* Fixed bug in Mt3dms.load to show correct error message when loading non-existent NAM file (545)
* Removed errant SFT parameter contained in Mt3dUzt.__init__ routine (572)
* Fixed DISV shapefile export bug that applied layer 1 parameter values to all model layers during export (508)
* Updated ModflowSfr2.load to store channel_geometry and channel_flow_data (6d, 6e) by nseg instead of itmp position (546)
* Fixed bug in ModflowMnw2.make_node_data to be able to set multiple wells with different numbers of nodes (556)
* Fixed bug reading MODFLOW 6 comma separated files (509)
* Fixed bug constructing a grid class with MODFLOW-USG (513)
* Optimized performance of grid class by minimizing redundant operations through use of data result caching (520)
* Fixed bug passing multiple auxiliary variables for MODFLOW 6 array data (533)
* Fixed bug in Mt3dUzt.__init__; the variable ioutobs doesn't exist in the UZT package and was removed.
* Fixed MODFLOW-LGR bug in which ascii files were not able to be created for some output. Added better testing of the MODFLOW-LGR capabilities to t035_test.py.
* Fixed multiple issues in mfdis that resulted in incorrect row column determination when using the method get_rc_from_node_coordinates (560). Added better testing of this to t007_test.py.
* Fixed the export_array_contours function as contours would not export in some cases (577). Added tests of export_array_contours and export_array to t007_test.py as these methods were not tested at all.

* Added support for the drain return package.
* Added support for pyshp version 2.x, which contains a different call signature for the writer than earlier versions.
* Added a new flopy3_MT3DMS_examples notebook, which uses Flopy to reproduce the example problems described in the MT3DMS documentation report by Zheng and Wang (1999).
* Pylint is now used on Travis for the Python 3.5 distribution to check for coding errors.
* Added testing with Python 3.7 on Travis, dropped testing Python 3.4.
* Added a new htop argument to the vtk writer, which allows cell tops to be defined by the simulated head.
* Generalized exporting and plotting to also work with MODFLOW 6. Added a new grid class and deprecated SpatialReference class. Added new plotting interfaces, `PlotMapView` and `PlotCrossSection`. Began deprecation of `ModelMap` and `ModelCrossSection` classes.
* Spatial reference system cache moved to epsgref.json in the user's data directory.
* Attempts to read empty files from flopy.utils raise a IOError exception.
* Changed interface for creating and accessing MODFLOW 6 observation, time series, and time array series packages. These packages can now be created and accessed directly from the package that references them. These changes are not backward compatible, and will require existing scripts to be modified. See the flopy3_mf6_obs_ts_tas.ipynb notebook for instructions.
* Changed the MODFLOW 6 fname argument to be filename. This change is not backward compatible, and will require existing scripts to be modified if the fname argument was used in the package constructor.
* Added modflow-nwt options support for `ModflowWel`, `ModflowSfr2`, and `ModflowUzf1` via the `OptionBlock` class.

* Bug fixes:
* Removed variable MXUZCON from `mtuzt.py` that was present during the development of MT3D-USGS, but was not included in the release version of MT3D-USGS.
* Now account for UZT -> UZT2 changes with the release of MT3D-USGS 1.0.1. Use of UZT is no longer supported.
* Fixed bug in `mfuzf1.py` when reading and writing `surfk` when `specifysurfk = True`.
* Fixed bug in `ModflowStr.load()`, utility would fail to load when comments were present.
* Fixed bug in MNW2 in which nodes were not sorted correctly.
* Ensure that external 1-D free arrays are written on one line.
* Typos corrected for various functions, keyword arguments, property names, input file options, and documentation.

* Added parameter_load variable to `mbase` that is set to true if parameter data are applied in the model (only used in models that support parameters). If this is set to `True` `free_format_input` is set to `True` (if currently `False`) when the `write_input()` method is called. This change preserves the precision of parameter data (which is free format data).
* MODFLOW 6 model and simulation packages can not be retrieved as a `MFSimulation` attribute
* Added support for multicomponent load in `mfsft.py`
* Added functionality to read esri-style epsg codes from [spatialreference.org](http://spatialreference.org).
* Added functionality to MODFLOW 6 that will automatically replace the existing package with the one being added if it has the same name as the existing package.
* Added separate MODFLOW 6 model classes for each model type. Model classes contain name file options.
* Added standard `run_model()` method arguments to mf6 `run_simulation()` method.
* some performance improvements to checking
* `SpatialReference.export_array()` now writes 3-D numpy arrays to multiband GeoTiffs
* Add load support to for MNW1; ModflowMnw1 now uses a `stress_period_data` `Mflist` to store MNW information, similar to other BC packages.
* Added a Triangle class that is a light wrapper for the Triangle program for generating triangular meshes. Added a notebook called flopy3_triangle.ipynb that demonstrates how to use it and build a MODFLOW 6 model with a triangular mesh. The current version of this Triangle class should be considered beta functionality as it is likely to change.
* Added support for MODPATH 7 (beta).
* Added support for MODPATH 3 and 5 pathline and endpoint output files.
* Added support for MODPATH timeseries output files (`flopy.utils.TimeseriesFile()`).
* Added support for plotting MODPATH timeseries output data (`plot_timeseries()`) with ModelMap.

* Bug fixes:
* Fixed issue in HOB when the same layer is specified in the `MLAY` data (dataset 4). If the layer exists the previous fraction value is added to the current value.
* Fixed bug in segment renumbering
* Changed default value for `ioutobs` `**kwargs` in `mtsft.py` from None to 0 to prevent failure.
* Fixed bug when passing extra components info from load to constructor in `mtsft.py` and `mtrct.py`.
* Fixed bug in `mt3ddsp` load - if `multidiffusion` is not found, should only read one 3d array.
* Fixed bug in `zonbud` utility that wasn't accumulating flow from constant heads.
* Fixed minor bug that precluded the passing of mass-balance record names (`TOTAL_IN`, `IN-OUT`, etc.).
* Fixed bug when writing shapefile projection (`.prj`) files using relative paths.
* Fixed bugs in `sfr.load()` -- `weight` and `flwtol` should be cast as floats, not integers.
* Fixed bug when `SpatialReference` supplied with geographic CRS.
* Fixed bug in `mfsfr.py` when writing kinematic data (`irtflg >0`).
* Fixed issue from change in MODFLOW 6 `inspect.getargspec()` method (for getting method arguments).
* Fixed MODFLOW 6 BINARY keyword for reading binary data from a file using `OPEN/CLOSE` (needs parentheses around it).
* Fixed bug in `mtlkt.py` when instatiating, loading, and/or writing lkt input file related to multi-species problems.