ci(release): set version to 3.5.0, update plugins from DFN files, upd…

…ate changelog
modflowpy · Nov 25, 2023 · 89698c5 · 89698c5
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diff --git a/.docs/md/version_changes.md b/.docs/md/version_changes.md
@@ -1,4 +1,80 @@
 # Changelog
+### Version 3.5.0
+
+#### New features
+
+* [feat(simulation+model options)](https://github.com/modflowpy/flopy/commit/a16a379ef61cc16594ac6ac9eadb5ce4c6a4cee1): Dynamically generate simulation options from simulation namefile dfn (#1842). Committed by spaulins-usgs on 2023-07-10.
+* [feat(binaryfile)](https://github.com/modflowpy/flopy/commit/79311120d0daeb3ba1281c70faf97fcd92a1fde5): Add reverse() method to HeadFile, CellBudgetFile (#1829). Committed by w-bonelli on 2023-07-29.
+* [feat(get-modflow)](https://github.com/modflowpy/flopy/commit/1cb7594d12a2aa385a567613e9f840de63ba7157): Allow specifying repo owner (#1910). Committed by w-bonelli on 2023-08-08.
+* [feat(generate_classes)](https://github.com/modflowpy/flopy/commit/e02030876c20d6bf588134bc0ab0cc1c75c0c46e): Create a command-line interface (#1912). Committed by Mike Taves on 2023-08-16.
+* [feat(gridutil)](https://github.com/modflowpy/flopy/commit/e20a29814afd97650d6ee2b10f0939893be64551): Add function to help create DISV grid (#1952). Committed by langevin-usgs on 2023-09-18.
+* [feat(pandas list)](https://github.com/modflowpy/flopy/commit/6a46a9b75286d7e268d4addc77946246ccb5db56): Fix for handling special case where boundname set but not used (#1982). Committed by scottrp on 2023-10-06.
+* [feat(MfSimulationList)](https://github.com/modflowpy/flopy/commit/b34f154362320059d92050b54014ec1fc9c9f09f): Add functionality to parse the mfsim.lst file (#2005). Committed by jdhughes-usgs on 2023-11-14.
+* [feat(modflow)](https://github.com/modflowpy/flopy/commit/be104c4a38d2b1f4acfbdd5a49a5b3ddb325f852): Support dataframe for pkg data (#2010). Committed by wpbonelli on 2023-11-22.
+* [feat(mfsimlist)](https://github.com/modflowpy/flopy/commit/121ca78f6073813cec082cfd01f483dad6838781): Add functionality to parse memory_print_options (#2009). Committed by jdhughes-usgs on 2023-11-22.
+
+#### Bug fixes
+
+* [fix(exchange and gnc package cellids)](https://github.com/modflowpy/flopy/commit/a84d88596f8b8e8f9f8fa074ad8fce626a84ebd0): #1866 (#1871). Committed by spaulins-usgs on 2023-07-11.
+* [fix(binaryfile/gridutil)](https://github.com/modflowpy/flopy/commit/90f87f2932e17955dee68ec53347c9d06178f94a): Avoid numpy deprecation warnings (#1868). Committed by w-bonelli on 2023-07-12.
+* [fix(binary)](https://github.com/modflowpy/flopy/commit/ed549798333cf2186516d55ffb1e9d9a537a4a0f): Fix binary header information (#1877). Committed by jdhughes-usgs on 2023-07-16.
+* [fix(time series)](https://github.com/modflowpy/flopy/commit/8b03916b55fb7a923d13648237147124d77f09f5): Fix for multiple time series attached to single package (#1867) (#1873). Committed by spaulins-usgs on 2023-07-20.
+* [fix(check)](https://github.com/modflowpy/flopy/commit/8c330a7890fe732c5489ce6a2d5184a7b2fb70ee): Check now works properly with confined conditions (#1880) (#1882). Committed by spaulins-usgs on 2023-07-27.
+* [fix(mtlistfile)](https://github.com/modflowpy/flopy/commit/9a22f639865b9d81716f7fcecdfe33b3e5a352a2): Fix reading MT3D budget (#1899). Committed by Ralf Junghanns on 2023-08-03.
+* [fix(check)](https://github.com/modflowpy/flopy/commit/68f0c3bafcd2c806f22b0f75e8d18cc5c4428aa2): Updated flopy's check to work with cellid -1 values (#1885). Committed by spaulins-usgs on 2023-08-06.
+* [fix(BaseModel)](https://github.com/modflowpy/flopy/commit/c25c0b34a173fa9788ccd7a0de16da2d02f96e6c): Don't suppress error if exe not found (#1901). Committed by w-bonelli on 2023-08-07.
+* [fix(modelgrid)](https://github.com/modflowpy/flopy/commit/99f680feb39cb9450e1ce052024bb3da45e264d8): Retain crs data from classic nam files (#1904). Committed by Mike Taves on 2023-08-10.
+* [fix(keyword data)](https://github.com/modflowpy/flopy/commit/3cef778bdf979ac249d84d106ae7db01d5d8e391): Optional keywords (#1920). Committed by spaulins-usgs on 2023-08-16.
+* [fix(GridIntersect)](https://github.com/modflowpy/flopy/commit/f2064d8ce5d8bca6340c86b4947070031104104a): Combine list of geometries using unary_union (#1923). Committed by Mike Taves on 2023-08-21.
+* [fix(gridintersect)](https://github.com/modflowpy/flopy/commit/021ffaa8c406cda742f239673c4d1a802021b8b9): Add multilinestring tests (#1924). Committed by Davíd Brakenhoff on 2023-08-21.
+* [fix(binary file)](https://github.com/modflowpy/flopy/commit/66b0903f4812b6cef3020e7cdfd6e2c2d26f6d52): Was writing binary file information twice to external files (#1925) (#1928). Committed by scottrp on 2023-08-25.
+* [fix(ParticleData)](https://github.com/modflowpy/flopy/commit/5d57fb78b27238ea69adbdb3438c8e17db55ddad): Fix docstring, structured default is False (#1935). Committed by w-bonelli on 2023-08-25.
+* [fix(generate_classes)](https://github.com/modflowpy/flopy/commit/4f6cd47411b96460495b1f7d6582860a4d655060): Use branch arg if provided (#1938). Committed by w-bonelli on 2023-08-31.
+* [fix(remove_model)](https://github.com/modflowpy/flopy/commit/71855bdfcd37e95194b6e5928ae909a6f7ef15fa): Remove_model method fix and tests (#1945). Committed by scottrp on 2023-09-14.
+* [fix(export_contours/f)](https://github.com/modflowpy/flopy/commit/9e9d7302cd771ed305c96fbeb406e210c0d9aea7): Support matplotlib 3.8+ (#1951). Committed by wpbonelli on 2023-09-19.
+* [fix(resolve_exe)](https://github.com/modflowpy/flopy/commit/d7d7f6649118a84d869522b52b20a4af8a397ebe): Support extensionless abs/rel paths on windows (#1957). Committed by wpbonelli on 2023-09-24.
+* [fix(model_splitter.py)](https://github.com/modflowpy/flopy/commit/5b5eb4ec20c833df4117415d433513bf3a1b4aa5): Standardizing naming of iuzno, rno, lakeno, & wellno to ifno (#1963). Committed by Eric Morway on 2023-09-25.
+* [fix(mbase)](https://github.com/modflowpy/flopy/commit/637632cfa3ddbd2629dfc257759d36b851ee0063): Warn if duplicate pkgs or units (#1964). Committed by wpbonelli on 2023-09-26.
+* [fix(get_structured_faceflows)](https://github.com/modflowpy/flopy/commit/158d2d69fdfdd2cefbcdaa1a403f9103f51d2d70): Cover edge cases, expand tests (#1968). Committed by wpbonelli on 2023-09-29.
+* [fix(CellBudgetFile)](https://github.com/modflowpy/flopy/commit/4b105e866e4c58380415a25d131e9d96fc82a4ba): Detect compact fmt by negative nlay (#1966). Committed by wpbonelli on 2023-09-30.
+* [fix(pandas list)](https://github.com/modflowpy/flopy/commit/f77989d33955baa76032d9341226385215e45821): Deal with cellids with inconsistent types (#1980). Committed by scottrp on 2023-10-06.
+* [fix(model_splitter)](https://github.com/modflowpy/flopy/commit/5ebc216822a86f32c7a2ab9a3735f021475dc0f4): Check keys in mftransient array (#1998). Committed by jdhughes-usgs on 2023-11-13.
+* [fix(benchmarks)](https://github.com/modflowpy/flopy/commit/16183c3059f4a9bb10d74423500b566eb41d3d6e): Fix benchmark post-processing (#2004). Committed by wpbonelli on 2023-11-14.
+* [fix(MfSimulationList)](https://github.com/modflowpy/flopy/commit/7cc5e6f0b4861e2f9d85eb1e25592721d0427227): Add missing seek to get_runtime method (#2006). Committed by mjr-deltares on 2023-11-15.
+* [fix(get_disu_kwargs)](https://github.com/modflowpy/flopy/commit/419ae0e0c15b4f95f6ea334fe49f79e29917130b): Incorrect indexing of delr and delc (#2011). Committed by langevin-usgs on 2023-11-21.
+* [fix(PlotCrossSection)](https://github.com/modflowpy/flopy/commit/6e3c7911c1e94a9f8c36563662471c68a7aeeefc): Boundary conditions not plotting for DISU (#2012). Committed by langevin-usgs on 2023-11-21.
+* [fix(release.yml)](https://github.com/modflowpy/flopy/commit/11f518cd68be596c3f07b052f9d3320880c38170): Don't regenerate pkgs from mf6 main on release (#2014). Committed by wpbonelli on 2023-11-24.
+* [fix(release.yml)](https://github.com/modflowpy/flopy/commit/0da6b8ecc9087cc9c68a7d90999f61eb78f0f9ac): Fix update changelog step (#2015). Committed by wpbonelli on 2023-11-25.
+
+#### Refactoring
+
+* [refactor(_set_neighbors)](https://github.com/modflowpy/flopy/commit/9168b3a538a5f604010ad5df17ea7e868b8f913f): Check for closed iverts and remove closing ivert (#1876). Committed by Joshua Larsen on 2023-07-14.
+* [refactor(crs)](https://github.com/modflowpy/flopy/commit/02fae7d8084f52e852722338038b6ef7a2691e61): Provide support without pyproj, other deprecations (#1850). Committed by Mike Taves on 2023-07-19.
+* [refactor(Notebooks)](https://github.com/modflowpy/flopy/commit/c261ee8145e2791be2c2cc944e5a55cf19ef1560): Apply pyformat and black QA tools (#1879). Committed by Mike Taves on 2023-07-24.
+* [refactor](https://github.com/modflowpy/flopy/commit/8c3d7dbbaa753893d746965f9ecc48dc68b274cd): Require pandas>=2.0.0 as core dependency (#1887). Committed by w-bonelli on 2023-08-01.
+* [refactor(expired deprecation)](https://github.com/modflowpy/flopy/commit/47e5e359037518f29d14469531db68999d308a0f): Raise AttributeError with Grid.thick and Grid.saturated_thick (#1884). Committed by Mike Taves on 2023-08-01.
+* [refactor(pathline/endpoint plots)](https://github.com/modflowpy/flopy/commit/54d6099eb71a7789121bcfde8816b23fa06c258e): Support recarray or dataframe (#1888). Committed by w-bonelli on 2023-08-01.
+* [refactor(expired deprecation)](https://github.com/modflowpy/flopy/commit/70b9a37153bf51be7cc06db513b24950ce122fd2): Remove warning for third parameter of Grid.intersect (#1883). Committed by Mike Taves on 2023-08-01.
+* [refactor(dependencies)](https://github.com/modflowpy/flopy/commit/dd77e72b9676be8834dcf0a08e6f55fd35e2bc29): Constrain sphinx >=4 (#1898). Committed by w-bonelli on 2023-08-02.
+* [refactor(dependencies)](https://github.com/modflowpy/flopy/commit/03fa01fe09db45e30fe2faf4c5160622b78f1b24): Constrain sphinx-rtd-theme >=1 (#1900). Committed by w-bonelli on 2023-08-03.
+* [refactor(mf6)](https://github.com/modflowpy/flopy/commit/809e624fe77c4d112e482698434e2199345e68c2): Remove deprecated features (#1894). Committed by w-bonelli on 2023-08-03.
+* [refactor(plotutil)](https://github.com/modflowpy/flopy/commit/cf675c6b892a0d484f91465a4ad6600ffe4d518e): Remove deprecated utilities (#1891). Committed by w-bonelli on 2023-08-03.
+* [refactor(shapefile_utils)](https://github.com/modflowpy/flopy/commit/6f2da88f9b2d53f94f9c003ddfde3daf6952e3ba): Remove deprecated SpatialReference usages (#1892). Committed by w-bonelli on 2023-08-03.
+* [refactor(vtk)](https://github.com/modflowpy/flopy/commit/ca838b17e89114be8952d07e85d88b128d2ec2c3): Remove deprecated export_* functions (#1890). Committed by w-bonelli on 2023-08-03.
+* [refactor(generate_classes)](https://github.com/modflowpy/flopy/commit/72370269e2d6933245c65b3c93beb532016593f3): Deprecate branch for ref, introduce repo, test commit hashes (#1907). Committed by w-bonelli on 2023-08-09.
+* [refactor(expired deprecation)](https://github.com/modflowpy/flopy/commit/ed3a0cd68ad1acb68fba750f415fa095a19b741a): Remaining references to SpatialReference (#1914). Committed by Mike Taves on 2023-08-11.
+* [refactor(Mf6Splitter)](https://github.com/modflowpy/flopy/commit/3a1ae0bba3171561f0b4b78a2bb892fdd0c55e90): Control record and additional splitting checks (#1919). Committed by Joshua Larsen on 2023-08-21.
+* [refactor(triangle)](https://github.com/modflowpy/flopy/commit/9ca601259604b1805d8ec1a30b0a883a7b5f019a): Raise if output files not found (#1954). Committed by wpbonelli on 2023-09-22.
+* [refactor(recarray_utils)](https://github.com/modflowpy/flopy/commit/941a5f105b10f50fc71b14ea05abf499c4f65fa5): Deprecate functions, use numpy builtins (#1960). Committed by wpbonelli on 2023-09-27.
+* [refactor(contour_array)](https://github.com/modflowpy/flopy/commit/4ed68a2be1e6b4f607e27c38ce5eab9f66492e3f): Add layer param, update docstrings, expand tests (#1975). Committed by wpbonelli on 2023-10-18.
+* [refactor(model_splitter.py)](https://github.com/modflowpy/flopy/commit/4ef699e10b1fbd80055b85ca00a17b96d1c627ce): (#1994). Committed by Joshua Larsen on 2023-11-01.
+* [refactor(modflow)](https://github.com/modflowpy/flopy/commit/696a209416f91bc4a9e61b4392f4218e9bd83408): Remove deprecated features (#1893). Committed by wpbonelli on 2023-11-03.
+* [refactor](https://github.com/modflowpy/flopy/commit/af8954b45903680a2931573453228b03ea7beb6b): Support python3.12, simplify tests and dependencies (#1999). Committed by wpbonelli on 2023-11-13.
+* [refactor(msfsr2)](https://github.com/modflowpy/flopy/commit/4eea1870cb27aa2976cbf5366a6c2cb942a2f0c4): Write sfr_botm_conflicts.chk to model workspace (#2002). Committed by wpbonelli on 2023-11-14.
+* [refactor(shapefile_utils)](https://github.com/modflowpy/flopy/commit/0f8b521407694442c3bb2e50ce3d4f6207f86e48): Warn if fieldname truncated per 10 char limit (#2003). Committed by wpbonelli on 2023-11-14.
+* [refactor(pakbase)](https://github.com/modflowpy/flopy/commit/09b59ce8c0e33b32727e0f07e44efadf166ffba2): Standardize ipakcb docstrings/defaults (#2001). Committed by wpbonelli on 2023-11-22.
+* [refactor(.gitattributes)](https://github.com/modflowpy/flopy/commit/338f6d073d6ba7edecc12405f3da83ea51e6cc26): Exclude examples/data from linguist (#2017). Committed by wpbonelli on 2023-11-25.
+
 ### Version 3.4.3
 
 #### Bug fixes

diff --git a/CITATION.cff b/CITATION.cff
@@ -3,8 +3,8 @@ message: If you use this software, please cite both the article from preferred-c
   references, and the software itself.
 type: software
 title: FloPy
-version: 3.5.0.dev0
-date-released: '2023-09-30'
+version: 3.5.0
+date-released: '2023-11-25'
 doi: 10.5066/F7BK19FH
 abstract: A Python package to create, run, and post-process MODFLOW-based models.
 repository-artifact: https://pypi.org/project/flopy
@@ -80,35 +80,35 @@ preferred-citation:
   year: 2023
   month: 5
 references:
-  - authors:
-      - family-names: Bakker
-        given-names: Mark
-        orcid: https://orcid.org/0000-0002-5629-2861
-      - family-names: Post
-        given-names: Vincent
-        orcid: https://orcid.org/0000-0002-9463-3081
-      - family-names: Langevin
-        given-names: Christian D.
-        orcid: https://orcid.org/0000-0001-5610-9759
-      - family-names: Hughes
-        given-names: Joseph D.
-        orcid: https://orcid.org/0000-0003-1311-2354
-      - family-names: White
-        given-names: Jeremy T.
-        orcid: https://orcid.org/0000-0002-4950-1469
-      - family-names: Starn
-        given-names: Jon Jeffrey
-        orcid: https://orcid.org/0000-0001-5909-0010
-      - family-names: Fienen
-        given-names: Michael N.
-        orcid: https://orcid.org/0000-0002-7756-4651
-    type: article
-    title: Scripting MODFLOW Model Development Using Python and FloPy
-    doi: 10.1111/gwat.12413
-    journal: Groundwater
-    volume: 54
-    issue: 5
-    start: 733
-    end: 739
-    year: 2016
-    month: 9
+- authors:
+  - family-names: Bakker
+    given-names: Mark
+    orcid: https://orcid.org/0000-0002-5629-2861
+  - family-names: Post
+    given-names: Vincent
+    orcid: https://orcid.org/0000-0002-9463-3081
+  - family-names: Langevin
+    given-names: Christian D.
+    orcid: https://orcid.org/0000-0001-5610-9759
+  - family-names: Hughes
+    given-names: Joseph D.
+    orcid: https://orcid.org/0000-0003-1311-2354
+  - family-names: White
+    given-names: Jeremy T.
+    orcid: https://orcid.org/0000-0002-4950-1469
+  - family-names: Starn
+    given-names: Jon Jeffrey
+    orcid: https://orcid.org/0000-0001-5909-0010
+  - family-names: Fienen
+    given-names: Michael N.
+    orcid: https://orcid.org/0000-0002-7756-4651
+  type: article
+  title: Scripting MODFLOW Model Development Using Python and FloPy
+  doi: 10.1111/gwat.12413
+  journal: Groundwater
+  volume: 54
+  issue: 5
+  start: 733
+  end: 739
+  year: 2016
+  month: 9
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 
 <img src="https://raw.githubusercontent.com/modflowpy/flopy/master/examples/images/flopy3.png" alt="flopy3" style="width:50;height:20">
 
-### Version 3.5.0.dev0 (preliminary)
+### Version 3.5.0
 [![flopy continuous integration](https://github.com/modflowpy/flopy/actions/workflows/commit.yml/badge.svg?branch=develop)](https://github.com/modflowpy/flopy/actions/workflows/commit.yml)
 [![Read the Docs](https://github.com/modflowpy/flopy/actions/workflows/rtd.yml/badge.svg?branch=develop)](https://github.com/modflowpy/flopy/actions/workflows/rtd.yml)
 
@@ -142,7 +142,7 @@ How to Cite
 
 ##### ***Software/Code citation for FloPy:***
 
-[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., Brakenhoff, D. A., and Bonelli, W. P., 2023, FloPy v3.5.0.dev0 (preliminary): U.S. Geological Survey Software Release, 30 September 2023, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)
+[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., Brakenhoff, D. A., and Bonelli, W. P., 2023, FloPy v3.5.0: U.S. Geological Survey Software Release, 25 November 2023, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)
 
 
 Additional FloPy Related Publications
@@ -167,12 +167,10 @@ MODFLOW Resources
 Disclaimer
 ----------
 
-This software is preliminary or provisional and is subject to revision. It is 
-being provided to meet the need for timely best science. This software is 
-provided "as is" and "as-available", and makes no representations or warranties 
-of any kind concerning the software, whether express, implied, statutory, or 
-other. This includes, without limitation, warranties of title, 
-merchantability, fitness for a particular purpose, non-infringement, absence 
-of latent or other defects, accuracy, or the presence or absence of errors, 
-whether or not known or discoverable.
+This software is provided "as is" and "as-available", and makes no 
+representations or warranties of any kind concerning the software, whether 
+express, implied, statutory, or other. This includes, without limitation, 
+warranties of title, merchantability, fitness for a particular purpose, 
+non-infringement, absence of latent or other defects, accuracy, or the 
+presence or absence of errors, whether or not known or discoverable.
 
diff --git a/autotest/test_gridutil.py b/autotest/test_gridutil.py
@@ -86,16 +86,23 @@ def test_get_lni_infers_layer_count_when_int_ncpl(ncpl, nodes, expected):
             1,  # nlay
             3,  # nrow
             4,  # ncol
-            np.array(4 * [4.]),  # delr
-            np.array(3 * [3.]),  # delc
+            np.array(4 * [4.0]),  # delr
+            np.array(3 * [3.0]),  # delc
             np.array([-10]),  # top
             np.array([-30.0]),  # botm
         ),
     ],
 )
 def test_get_disu_kwargs(nlay, nrow, ncol, delr, delc, tp, botm):
     kwargs = get_disu_kwargs(
-        nlay=nlay, nrow=nrow, ncol=ncol, delr=delr, delc=delc, tp=tp, botm=botm, return_vertices=True
+        nlay=nlay,
+        nrow=nrow,
+        ncol=ncol,
+        delr=delr,
+        delc=delc,
+        tp=tp,
+        botm=botm,
+        return_vertices=True,
     )
 
     from pprint import pprint

diff --git a/code.json b/code.json
@@ -1,6 +1,6 @@
 [
     {
-        "status": "Preliminary",
+        "status": "Release",
         "languages": [
             "python"
         ],
@@ -29,9 +29,9 @@
         "downloadURL": "https://code.usgs.gov/usgs/modflow/flopy/archive/master.zip",
         "vcs": "git",
         "laborHours": -1,
-        "version": "3.5.0.dev0",
+        "version": "3.5.0",
         "date": {
-            "metadataLastUpdated": "2023-09-30"
+            "metadataLastUpdated": "2023-11-25"
         },
         "organization": "U.S. Geological Survey",
         "permissions": {