fix(dist): multiple fixes following review (#1573)

* omit utils/idmloader subdir
* update distribution checks
* rerun mf6ivar.py to update mf6io files
* fix typo in gwf-maw.dfn (missing and)
* use latex-friendly quotes in gwf-rcha dfn and tex description

.github/workflows/release.yml

@@ -346,7 +346,8 @@ jobs:
           cp modflow6/meson.build "$distname/meson.build"
           cp -r modflow6-examples/examples "$distname"
           cp -r modflow6/src "$distname"
-          cp -r modflow6/utils "$distname"
+          cp -r modflow6/utils/mf5to6 "$distname/utils/mf5to6"
+          cp -r modflow6/utils/zonebudget "$distname/utils/zonebudget"
           
           # create LaTeX file describing the folder structure
           cd modflow6/doc/ReleaseNotes

distribution/build_dist.py

@@ -1,13 +1,12 @@
 import argparse
 import os
 import platform
-import shutil
 import sys
 import textwrap
 from os import PathLike, environ
 from pathlib import Path
 from pprint import pprint
-from shutil import copytree
+from shutil import copy, copyfile, copytree, ignore_patterns
 
 import pytest
 from modflow_devtools.build import meson_build
@@ -16,8 +15,11 @@
 from modflow_devtools.misc import get_model_paths
 
 from build_docs import build_documentation
-from build_makefiles import (build_mf5to6_makefile, build_mf6_makefile,
-                             build_zbud6_makefile)
+from build_makefiles import (
+    build_mf5to6_makefile,
+    build_mf6_makefile,
+    build_zbud6_makefile,
+)
 from utils import get_project_root_path, run_command
 
 # default paths
@@ -54,31 +56,32 @@ def copy_sources(output_path: PathLike):
         str(source_msvs_path / "mf6bmi.sln"),
         str(source_msvs_path / "mf6bmi.vfproj"),
     ]:
-        shutil.copy(d, output_path / "msvs")
+        copy(d, output_path / "msvs")
 
-    ignored = shutil.ignore_patterns(".DS_Store")
+    ignored = [".DS_Store"]
 
     # copy top-level meson.build and meson.options
-    shutil.copy(_project_root_path / "meson.build", output_path)
-    shutil.copy(_project_root_path / "meson.options", output_path)
+    copy(_project_root_path / "meson.build", output_path)
+    copy(_project_root_path / "meson.options", output_path)
 
     # copy source folder
     src_path = _project_root_path / "src"
     dst_path = output_path / "src"
     print(f"Copying {src_path} to {dst_path}")
-    copytree(src_path, dst_path, ignore=ignored)
+    copytree(src_path, dst_path, ignore=ignore_patterns(*ignored))
 
     # copy srcbmi folder
     src_path = _project_root_path / "srcbmi"
     dst_path = output_path / "srcbmi"
     print(f"Copying {src_path} to {dst_path}")
-    copytree(src_path, dst_path, ignore=ignored)
+    copytree(src_path, dst_path, ignore=ignore_patterns(*ignored))
 
     # copy utils folder
     src_path = _project_root_path / "utils"
     dst_path = output_path / "utils"
     print(f"Copying {src_path} to {dst_path}")
-    copytree(src_path, dst_path, ignore=ignored)
+    ignored.extend(["idmloader"])
+    copytree(src_path, dst_path, ignore=ignore_patterns(*ignored))
 
 
 def test_copy_sources(tmp_path):
@@ -94,6 +97,14 @@ def test_copy_sources(tmp_path):
     assert (tmp_path / "utils" / "meson.build").is_file()
     assert (tmp_path / "msvs" / "mf6.sln").is_file()
 
+    assert (tmp_path / "utils").is_dir()
+    assert (tmp_path / "utils" / "mf5to6").is_dir()
+    assert (tmp_path / "utils" / "zonebudget").is_dir()
+    assert (tmp_path / "utils" / "mf5to6" / "pymake").is_dir()
+    assert (tmp_path / "utils" / "zonebudget" / "pymake").is_dir()
+    assert not (tmp_path / "utils" / "idmloader").is_dir()
+
+
 
 def build_examples(examples_repo_path: PathLike, overwrite: bool = False):
     examples_repo_path = Path(examples_repo_path).expanduser().absolute()
@@ -234,10 +245,10 @@ def build_makefiles(output_path: PathLike):
     # create and copy mf6 makefile
     build_mf6_makefile()
     (output_path / "make").mkdir(parents=True, exist_ok=True)
-    shutil.copyfile(
+    copyfile(
         _project_root_path / "make" / "makefile", output_path / "make" / "makefile"
     )
-    shutil.copyfile(
+    copyfile(
         _project_root_path / "make" / "makedefaults",
         output_path / "make" / "makedefaults",
     )
@@ -246,10 +257,10 @@ def build_makefiles(output_path: PathLike):
     build_zbud6_makefile()
     rel_path = Path("utils") / "zonebudget" / "make"
     (output_path / rel_path).mkdir(parents=True, exist_ok=True)
-    shutil.copyfile(
+    copyfile(
         _project_root_path / rel_path / "makefile", output_path / rel_path / "makefile"
     )
-    shutil.copyfile(
+    copyfile(
         _project_root_path / rel_path / "makedefaults",
         output_path / rel_path / "makedefaults",
     )
@@ -258,10 +269,10 @@ def build_makefiles(output_path: PathLike):
     build_mf5to6_makefile()
     rel_path = Path("utils") / "mf5to6" / "make"
     (output_path / rel_path).mkdir(parents=True, exist_ok=True)
-    shutil.copyfile(
+    copyfile(
         _project_root_path / rel_path / "makefile", output_path / rel_path / "makefile"
     )
-    shutil.copyfile(
+    copyfile(
         _project_root_path / rel_path / "makedefaults",
         output_path / rel_path / "makedefaults",
     )
@@ -301,7 +312,7 @@ def build_distribution(
     )
 
     # code.json metadata
-    shutil.copy(_project_root_path / "code.json", output_path)
+    copy(_project_root_path / "code.json", output_path)
 
     # full releases include examples, source code, makefiles and docs
     if not full:

distribution/check_dist.py

@@ -75,8 +75,11 @@ def test_sources(dist_dir_path, releasemode, full):
     if not full:
         pytest.skip(reason="sources not included in minimal distribution")
 
+    # check top-level meson files
     assert (dist_dir_path / "meson.build").is_file()
     assert (dist_dir_path / "meson.options").is_file()
+
+    # check src subdir
     assert (dist_dir_path / "src").is_dir()
     assert (dist_dir_path / "src" / "mf6.f90").is_file()
     version_file_path = dist_dir_path / "src" / "Utilities" / "version.f90"
@@ -90,6 +93,14 @@ def test_sources(dist_dir_path, releasemode, full):
     idevelopmode = 0 if releasemode else 1
     assert f"IDEVELOPMODE = {idevelopmode}" in line
 
+    # check utils subdir
+    assert (dist_dir_path / "utils").is_dir()
+    assert (dist_dir_path / "utils" / "mf5to6").is_dir()
+    assert (dist_dir_path / "utils" / "zonebudget").is_dir()
+    assert (dist_dir_path / "utils" / "mf5to6" / "pymake").is_dir()
+    assert (dist_dir_path / "utils" / "zonebudget" / "pymake").is_dir()
+    assert not (dist_dir_path / "utils" / "idmloader").is_dir()
+
 
 @pytest.mark.skipif(not _fc, reason="needs Fortran compiler")
 def test_makefiles(dist_dir_path, full):

doc/mf6io/mf6ivar/dfn/gwf-maw.dfn

@@ -485,7 +485,7 @@ tagged false
 in_record true
 reader urword
 longname screen bottom
-description value that defines the bottom elevation of the screen for the multi-aquifer well connection. If CONDEQN is SPECIFIED, THIEM, SKIN, or COMPOSITE, SCRN\_BOT can be any value is set to the bottom of the cell. If CONDEQN is MEAN, SCRN\_BOT is set to the multi-aquifer well connection cell bottom if the specified value is less than the cell bottom. The program will terminate with an error if the screen bottom is greater than the screen top.
+description value that defines the bottom elevation of the screen for the multi-aquifer well connection. If CONDEQN is SPECIFIED, THIEM, SKIN, or COMPOSITE, SCRN\_BOT can be any value and is set to the bottom of the cell. If CONDEQN is MEAN, SCRN\_BOT is set to the multi-aquifer well connection cell bottom if the specified value is less than the cell bottom. The program will terminate with an error if the screen bottom is greater than the screen top.
 
 block connectiondata
 name hk_skin

doc/mf6io/mf6ivar/dfn/gwf-rcha.dfn

@@ -107,7 +107,7 @@ reader urword
 optional false
 tagged false
 longname file name of time series information
-description defines a time-array-series file defining a time-array series that can be used to assign time-varying values. See the Time-Variable Input section for instructions on using the time-array series capability.
+description defines a time-array-series file defining a time-array series that can be used to assign time-varying values. See the ``Time-Variable Input'' section for instructions on using the time-array series capability.
 
 block options
 name obs_filerecord