From acc56ba548fa1c4f45c89eca68481fba6eaa9fbd Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 12 Sep 2023 01:10:39 +0000
Subject: [PATCH 01/12] ci(release): update to development version 1.3.0.dev0

---
 docs/conf.py                 | 2 +-
 modflow_devtools/__init__.py | 2 +-
 version.txt                  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index ba8c65b..5b64ea9 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -8,7 +8,7 @@
 
 project = "modflow-devtools"
 author = "MODFLOW Team"
-release = "1.2.0"
+release = "1.3.0.dev0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/modflow_devtools/__init__.py b/modflow_devtools/__init__.py
index a37151c..436d4e8 100644
--- a/modflow_devtools/__init__.py
+++ b/modflow_devtools/__init__.py
@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
 __date__ = "Sep 12, 2023"
-__version__ = "1.2.0"
+__version__ = "1.3.0.dev0"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "jdhughes@usgs.gov"
 __status__ = "Production"
diff --git a/version.txt b/version.txt
index 867e524..14c65ab 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-1.2.0
\ No newline at end of file
+1.3.0.dev0
\ No newline at end of file

From 2095ced3b3955a98f21c49756b359441878c0a4b Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Tue, 12 Sep 2023 09:25:37 -0400
Subject: [PATCH 02/12] ci: update release.yml for trusted publishing to PyPI
 (#115)

---
 .github/workflows/release.yml | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index ad286b2..7a2bd3a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -164,6 +164,10 @@ jobs:
     permissions:
       contents: write
       pull-requests: write
+      id-token: write  # mandatory for trusted publishing
+    environment:  # requires a 'release' environment in repo settings
+      name: release
+      url: https://pypi.org/p/modflow-devtools
     steps:
 
       - name: Checkout main branch
@@ -188,12 +192,14 @@ jobs:
       - name: Check package
         run: twine check --strict dist/*
 
-      - name: Publish package
-        if: ${{ env.TWINE_USERNAME != '' }}
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: twine upload dist/*
+      - name: Upload package
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
 
   reset:
     name: Draft reset PR

From 0ce571411b6b35bc62d4f333d1a961bd2f202784 Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Tue, 12 Sep 2023 10:46:51 -0400
Subject: [PATCH 03/12] feat(fixtures): add --tabular pytest CLI arg and
 corresponding fixture (#116)

---
 modflow_devtools/fixtures.py           | 19 +++++++++++++++-
 modflow_devtools/test/test_fixtures.py | 31 ++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 1 deletion(-)

diff --git a/modflow_devtools/fixtures.py b/modflow_devtools/fixtures.py
index 1fa695c..0700cf8 100644
--- a/modflow_devtools/fixtures.py
+++ b/modflow_devtools/fixtures.py
@@ -101,6 +101,14 @@ def use_pandas(request):
         raise ValueError(f"Unsupported value for --pandas: {pandas}")
 
 
+@pytest.fixture
+def tabular(request):
+    tab = request.config.option.TABULAR
+    if tab not in ["raw", "recarray", "dataframe"]:
+        raise ValueError(f"Unsupported value for --tabular: {tab}")
+    return tab
+
+
 # configuration hooks
 
 
@@ -163,7 +171,16 @@ def pytest_addoption(parser):
         action="store",
         default="yes",
         dest="PANDAS",
-        help="Package input data can be provided as either pandas dataframes or numpy recarrays. By default, pandas dataframes are used. To test with numpy recarrays, use 'no'. To randomize selection (per test), use 'random'.",
+        help="Indicates whether to use pandas, where multiple approaches are available. Select 'yes', 'no', or 'random'.",
+    )
+
+    parser.addoption(
+        "-T",
+        "--tabular",
+        action="store",
+        default="raw",
+        dest="TABULAR",
+        help="Configure tabular data representation for model input. Select 'raw', 'recarray', or 'dataframe'.",
     )
 
 
diff --git a/modflow_devtools/test/test_fixtures.py b/modflow_devtools/test/test_fixtures.py
index c5364e6..32d0f46 100644
--- a/modflow_devtools/test/test_fixtures.py
+++ b/modflow_devtools/test/test_fixtures.py
@@ -316,3 +316,34 @@ def test_pandas(pandas, arg, function_tmpdir):
         assert "True" in res
     elif pandas == "no":
         assert "False" in res
+
+
+test_tabular_fname = "tabular.txt"
+
+
+@pytest.mark.meta("test_tabular")
+def test_tabular_inner(function_tmpdir, tabular):
+    with open(function_tmpdir / test_tabular_fname, "w") as f:
+        f.write(str(tabular))
+
+
+@pytest.mark.parametrize("tabular", ["raw", "recarray", "dataframe"])
+@pytest.mark.parametrize("arg", ["--tabular", "-T"])
+def test_tabular(tabular, arg, function_tmpdir):
+    inner_fn = test_tabular_inner.__name__
+    args = [
+        __file__,
+        "-v",
+        "-s",
+        "-k",
+        inner_fn,
+        arg,
+        tabular,
+        "--keep",
+        function_tmpdir,
+        "-M",
+        "test_tabular",
+    ]
+    assert pytest.main(args) == ExitCode.OK
+    res = open(next(function_tmpdir.rglob(test_tabular_fname))).readlines()[0]
+    assert tabular == res

From 506a238f6f31d827015a6c6f5ba1867ee55948a7 Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Tue, 12 Sep 2023 18:03:19 -0400
Subject: [PATCH 04/12] feat(timeit): add function timing decorator (#118)

---
 docs/index.rst                     |  1 +
 docs/md/timeit.md                  | 17 ++++++++++++++
 modflow_devtools/misc.py           | 37 ++++++++++++++++++++++++++++++
 modflow_devtools/test/test_misc.py | 24 +++++++++++++++++++
 4 files changed, 79 insertions(+)
 create mode 100644 docs/md/timeit.md

diff --git a/docs/index.rst b/docs/index.rst
index cbeaa40..393f81b 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -31,6 +31,7 @@ The `modflow-devtools` package provides a set of tools for developing and testin
    md/download.md
    md/ostags.md
    md/zip.md
+   md/timeit.md
 
 
 .. toctree::
diff --git a/docs/md/timeit.md b/docs/md/timeit.md
new file mode 100644
index 0000000..c57ef85
--- /dev/null
+++ b/docs/md/timeit.md
@@ -0,0 +1,17 @@
+# `timeit`
+
+There is a `timeit` decorator function available in the `modflow_devtools.misc` module. Applying it to any function causes a (rough) runtime benchmark to be printed to `stdout` afterwards the function returns. For instance:
+
+```python
+@timeit
+def sleep1():
+    sleep(0.001)
+
+sleep1() # prints e.g. "sleep1 took 1.26 ms"
+```
+
+`timeit` can also directly wrap a function:
+
+```python
+timeit(sleep1)() # prints same as above
+```
\ No newline at end of file
diff --git a/modflow_devtools/misc.py b/modflow_devtools/misc.py
index 7dd9210..284a6ed 100644
--- a/modflow_devtools/misc.py
+++ b/modflow_devtools/misc.py
@@ -1,8 +1,10 @@
 import importlib
 import socket
 import sys
+import time
 import traceback
 from contextlib import contextmanager
+from functools import wraps
 from importlib import metadata
 from os import PathLike, chdir, environ, getcwd
 from os.path import basename, normpath
@@ -442,3 +444,38 @@ def try_metadata() -> bool:
     _has_pkg_cache[pkg] = found
 
     return _has_pkg_cache[pkg]
+
+
+def timeit(f):
+    """
+    Decorator for estimating runtime of any function.
+    Prints estimated time to stdout, in milliseconds.
+
+    Parameters
+    ----------
+    f : function
+        Function to time.
+
+    Notes
+    -----
+    Adapted from https://stackoverflow.com/a/27737385/6514033.
+
+    Returns
+    -------
+    function
+        The decorated function.
+    """
+
+    @wraps(f)
+    def timed(*args, **kw):
+        ts = time.time()
+        res = f(*args, **kw)
+        te = time.time()
+        if "log_time" in kw:
+            name = kw.get("log_name", f.__name__.upper())
+            kw["log_time"][name] = int((te - ts) * 1000)
+        else:
+            print(f"{f.__name__} took {(te - ts) * 1000:.2f} ms")
+        return res
+
+    return timed
diff --git a/modflow_devtools/test/test_misc.py b/modflow_devtools/test/test_misc.py
index 79ea786..b8ebd40 100644
--- a/modflow_devtools/test/test_misc.py
+++ b/modflow_devtools/test/test_misc.py
@@ -1,8 +1,10 @@
 import os
+import re
 import shutil
 from os import environ
 from pathlib import Path
 from pprint import pprint
+from time import sleep
 from typing import List
 
 import pytest
@@ -15,6 +17,7 @@
     has_pkg,
     set_dir,
     set_env,
+    timeit,
 )
 
 
@@ -283,3 +286,24 @@ def test_has_pkg(virtualenv):
             ).strip()
             == exp
         )
+
+
+def test_timeit1(capfd):
+    def sleep1():
+        sleep(0.001)
+
+    timeit(sleep1)()
+    cap = capfd.readouterr()
+    print(cap.out)
+    assert re.match(r"sleep1 took \d+\.\d+ ms", cap.out)
+
+
+def test_timeit2(capfd):
+    @timeit
+    def sleep1dec():
+        sleep(0.001)
+
+    sleep1dec()
+    cap = capfd.readouterr()
+    print(cap.out)
+    assert re.match(r"sleep1dec took \d+\.\d+ ms", cap.out)

From d725ddb13bdfe4cee45865a7412811765714891a Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Tue, 12 Sep 2023 18:55:03 -0400
Subject: [PATCH 05/12] Revert "feat(timeit): add function timing decorator
 (#118)" (#119)

* reverts 506a238f6f31d827015a6c6f5ba1867ee55948a7.
---
 docs/index.rst                     |  1 -
 docs/md/timeit.md                  | 17 --------------
 modflow_devtools/misc.py           | 37 ------------------------------
 modflow_devtools/test/test_misc.py | 24 -------------------
 4 files changed, 79 deletions(-)
 delete mode 100644 docs/md/timeit.md

diff --git a/docs/index.rst b/docs/index.rst
index 393f81b..cbeaa40 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -31,7 +31,6 @@ The `modflow-devtools` package provides a set of tools for developing and testin
    md/download.md
    md/ostags.md
    md/zip.md
-   md/timeit.md
 
 
 .. toctree::
diff --git a/docs/md/timeit.md b/docs/md/timeit.md
deleted file mode 100644
index c57ef85..0000000
--- a/docs/md/timeit.md
+++ /dev/null
@@ -1,17 +0,0 @@
-# `timeit`
-
-There is a `timeit` decorator function available in the `modflow_devtools.misc` module. Applying it to any function causes a (rough) runtime benchmark to be printed to `stdout` afterwards the function returns. For instance:
-
-```python
-@timeit
-def sleep1():
-    sleep(0.001)
-
-sleep1() # prints e.g. "sleep1 took 1.26 ms"
-```
-
-`timeit` can also directly wrap a function:
-
-```python
-timeit(sleep1)() # prints same as above
-```
\ No newline at end of file
diff --git a/modflow_devtools/misc.py b/modflow_devtools/misc.py
index 284a6ed..7dd9210 100644
--- a/modflow_devtools/misc.py
+++ b/modflow_devtools/misc.py
@@ -1,10 +1,8 @@
 import importlib
 import socket
 import sys
-import time
 import traceback
 from contextlib import contextmanager
-from functools import wraps
 from importlib import metadata
 from os import PathLike, chdir, environ, getcwd
 from os.path import basename, normpath
@@ -444,38 +442,3 @@ def try_metadata() -> bool:
     _has_pkg_cache[pkg] = found
 
     return _has_pkg_cache[pkg]
-
-
-def timeit(f):
-    """
-    Decorator for estimating runtime of any function.
-    Prints estimated time to stdout, in milliseconds.
-
-    Parameters
-    ----------
-    f : function
-        Function to time.
-
-    Notes
-    -----
-    Adapted from https://stackoverflow.com/a/27737385/6514033.
-
-    Returns
-    -------
-    function
-        The decorated function.
-    """
-
-    @wraps(f)
-    def timed(*args, **kw):
-        ts = time.time()
-        res = f(*args, **kw)
-        te = time.time()
-        if "log_time" in kw:
-            name = kw.get("log_name", f.__name__.upper())
-            kw["log_time"][name] = int((te - ts) * 1000)
-        else:
-            print(f"{f.__name__} took {(te - ts) * 1000:.2f} ms")
-        return res
-
-    return timed
diff --git a/modflow_devtools/test/test_misc.py b/modflow_devtools/test/test_misc.py
index b8ebd40..79ea786 100644
--- a/modflow_devtools/test/test_misc.py
+++ b/modflow_devtools/test/test_misc.py
@@ -1,10 +1,8 @@
 import os
-import re
 import shutil
 from os import environ
 from pathlib import Path
 from pprint import pprint
-from time import sleep
 from typing import List
 
 import pytest
@@ -17,7 +15,6 @@
     has_pkg,
     set_dir,
     set_env,
-    timeit,
 )
 
 
@@ -286,24 +283,3 @@ def test_has_pkg(virtualenv):
             ).strip()
             == exp
         )
-
-
-def test_timeit1(capfd):
-    def sleep1():
-        sleep(0.001)
-
-    timeit(sleep1)()
-    cap = capfd.readouterr()
-    print(cap.out)
-    assert re.match(r"sleep1 took \d+\.\d+ ms", cap.out)
-
-
-def test_timeit2(capfd):
-    @timeit
-    def sleep1dec():
-        sleep(0.001)
-
-    sleep1dec()
-    cap = capfd.readouterr()
-    print(cap.out)
-    assert re.match(r"sleep1dec took \d+\.\d+ ms", cap.out)

From 8bb5f03f50139118cfb5829220d62aa3af157873 Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Fri, 29 Sep 2023 09:27:37 -0400
Subject: [PATCH 06/12] ci: enable colorful pytest output (#121)

---
 pytest.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pytest.ini b/pytest.ini
index 2e0fa86..93b6f6d 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,5 +1,5 @@
 [pytest]
-addopts = -ra
+addopts = -ra --color=yes
 python_files =
     test_*.py
     *_test*.py

From 2f4cdf28bdda685f99bbc60e043e418ff8c848d7 Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Fri, 29 Sep 2023 17:02:57 -0400
Subject: [PATCH 07/12] Revert "Revert "feat(timeit): add function timing
 decorator (#118)"" (#120)

* Revert "Revert "feat(timeit): add function timing decorator (#118)" (#119)"
* rename timeit -> timed, use builtin timeit module internally, update docs
---
 docs/index.rst                     |  1 +
 docs/md/timed.md                   | 21 +++++++++++++++
 modflow_devtools/misc.py           | 43 ++++++++++++++++++++++++++++++
 modflow_devtools/test/test_misc.py | 28 ++++++++++++++++---
 4 files changed, 90 insertions(+), 3 deletions(-)
 create mode 100644 docs/md/timed.md

diff --git a/docs/index.rst b/docs/index.rst
index cbeaa40..e71195d 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -31,6 +31,7 @@ The `modflow-devtools` package provides a set of tools for developing and testin
    md/download.md
    md/ostags.md
    md/zip.md
+   md/timed.md
 
 
 .. toctree::
diff --git a/docs/md/timed.md b/docs/md/timed.md
new file mode 100644
index 0000000..d4de7ab
--- /dev/null
+++ b/docs/md/timed.md
@@ -0,0 +1,21 @@
+# `timed`
+
+There is a `@timed` decorator function available in the `modflow_devtools.misc` module. Applying it to any function prints a (rough) benchmark to `stdout` when the function returns. For instance:
+
+```python
+from modflow_devtools.misc import timed
+
+@timed
+def sleep1():
+    sleep(0.001)
+
+sleep1() # prints e.g. "sleep1 took 1.26 ms"
+```
+
+It can also wrap a function directly:
+
+```python
+timed(sleep1)()
+```
+
+The [`timeit`](https://docs.python.org/3/library/timeit.html) built-in module is used internally, however the timed function is only called once, where by default, `timeit` averages multiple runs.
\ No newline at end of file
diff --git a/modflow_devtools/misc.py b/modflow_devtools/misc.py
index 7dd9210..9646aee 100644
--- a/modflow_devtools/misc.py
+++ b/modflow_devtools/misc.py
@@ -3,12 +3,14 @@
 import sys
 import traceback
 from contextlib import contextmanager
+from functools import wraps
 from importlib import metadata
 from os import PathLike, chdir, environ, getcwd
 from os.path import basename, normpath
 from pathlib import Path
 from shutil import which
 from subprocess import PIPE, Popen
+from timeit import timeit
 from typing import List, Optional, Tuple
 from urllib import request
 
@@ -442,3 +444,44 @@ def try_metadata() -> bool:
     _has_pkg_cache[pkg] = found
 
     return _has_pkg_cache[pkg]
+
+
+def timed(f):
+    """
+    Decorator for estimating runtime of any function.
+    Prints estimated time to stdout, in milliseconds.
+
+    Parameters
+    ----------
+    f : function
+        Function to time.
+
+    Notes
+    -----
+    Adapted from https://stackoverflow.com/a/27737385/6514033.
+    Uses the built-in timeit module internally.
+
+    Returns
+    -------
+    function
+        The decorated function.
+    """
+
+    @wraps(f)
+    def _timed(*args, **kw):
+        res = None
+
+        def call():
+            nonlocal res
+            res = f(*args, **kw)
+
+        t = timeit(lambda: call(), number=1)
+        if "log_time" in kw:
+            name = kw.get("log_name", f.__name__.upper())
+            kw["log_time"][name] = int(t * 1000)
+        else:
+            print(f"{f.__name__} took {t * 1000:.2f} ms")
+
+        return res
+
+    return _timed
diff --git a/modflow_devtools/test/test_misc.py b/modflow_devtools/test/test_misc.py
index 79ea786..ff4f980 100644
--- a/modflow_devtools/test/test_misc.py
+++ b/modflow_devtools/test/test_misc.py
@@ -1,8 +1,9 @@
 import os
+import re
 import shutil
 from os import environ
 from pathlib import Path
-from pprint import pprint
+from time import sleep
 from typing import List
 
 import pytest
@@ -12,9 +13,9 @@
     get_namefile_paths,
     get_packages,
     has_package,
-    has_pkg,
     set_dir,
     set_env,
+    timed,
 )
 
 
@@ -25,7 +26,7 @@ def test_set_dir(tmp_path):
     assert Path(os.getcwd()) != tmp_path
 
 
-def test_set_env(tmp_path):
+def test_set_env():
     # test adding a variable
     key = "TEST_ENV"
     val = "test"
@@ -283,3 +284,24 @@ def test_has_pkg(virtualenv):
             ).strip()
             == exp
         )
+
+
+def test_timed1(capfd):
+    def sleep1():
+        sleep(0.001)
+
+    timed(sleep1)()
+    cap = capfd.readouterr()
+    print(cap.out)
+    assert re.match(r"sleep1 took \d+\.\d+ ms", cap.out)
+
+
+def test_timed2(capfd):
+    @timed
+    def sleep1dec():
+        sleep(0.001)
+
+    sleep1dec()
+    cap = capfd.readouterr()
+    print(cap.out)
+    assert re.match(r"sleep1dec took \d+\.\d+ ms", cap.out)

From 48dda25ad43eb6d757d69416281ecb022f7dc4dd Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Mon, 9 Oct 2023 12:16:04 -0400
Subject: [PATCH 08/12] docs: minor corrections (#122)

---
 docs/md/download.md | 2 +-
 docs/md/ostags.md   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/md/download.md b/docs/md/download.md
index 9a3643b..069f0af 100644
--- a/docs/md/download.md
+++ b/docs/md/download.md
@@ -20,7 +20,7 @@ print([asset["name"] for asset in assets])
 
 This yields `['code.json', 'linux.zip', 'mac.zip', 'win64.zip']`.
 
-Equivalently, using the `list_release_assets()` function to list the latest release assets directly:
+Equivalently, using the `get_release_assets()` function to list the latest release assets directly:
 
 ```python
 from modflow_devtools.download import get_release_assets
diff --git a/docs/md/ostags.md b/docs/md/ostags.md
index ea9440c..6108dc7 100644
--- a/docs/md/ostags.md
+++ b/docs/md/ostags.md
@@ -46,11 +46,11 @@ The second argument specifies the mapping in format `<source>2<target>`, where `
 
 ## Getting suffixes
 
-A convenience function is available to get the appropriate binary file extensions for a given operating system, identified by tag (or the current operating system if no tag is provided). The return value is a 2-tuple containing the executable and library extensions, respectively.
+A convenience function is available to get the appropriate binary file extensions for a given operating system, identified by any supported OS tag, or the current operating system if no tag is provided. The return value is a 2-tuple containing the executable and library extensions, respectively.
 
 ```python
 get_binary_suffixes()  # get extensions for current OS
 get_binary_suffixes("linux")  # returns ("", ".so")
-get_binary_suffixes("linux")  # returns ("", ".so")
+get_binary_suffixes("mac")  # returns ("", ".dylib")
 get_binary_suffixes("win64")  # returns (".exe", ".dll")
 ```

From e464c40ba8a97c468a63f94b64f10e1ec5f2a4cd Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Wed, 18 Oct 2023 08:49:18 -0400
Subject: [PATCH 09/12] ci: remove branch filters from push trigger (#123)

---
 .github/workflows/ci.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4738d35..9ca7cb0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,15 +1,12 @@
 name: CI
 on:
   push:
-    branches:
-      - main
-      - develop*
     paths-ignore:
       - '**.md'
   pull_request:
     branches:
       - main
-      - develop*
+      - develop
     paths-ignore:
       - '**.md'
 jobs:

From cd644fa90885cde04f36f24e44cfe922b2a38897 Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Sat, 11 Nov 2023 00:09:48 -0500
Subject: [PATCH 10/12] refactor: support python 3.12, various updates (#124)

* add python 3.12 classifier to `pyproject.toml`
* explicitly specify packages in `pyproject.toml`
* add authors to `pyproject.toml`
* remove version fn from `Executables`
* move tests from main module to `autotest/`
* remove `BIN_PATH` testing environment variable
* remove testing dependency on mf6 & related exes
* remove `pytest-virtualenv` testing dependency
* add `.vscode/` to `.gitignore`
---
 .github/workflows/ci.yml                      | 26 ++----
 .gitignore                                    |  3 +-
 DEVELOPER.md                                  | 10 +--
 .../test => autotest}/__init__.py             |  0
 conftest.py => autotest/conftest.py           |  0
 pytest.ini => autotest/pytest.ini             |  2 +-
 .../test => autotest}/test_build.py           |  1 +
 .../test => autotest}/test_download.py        |  1 +
 autotest/test_executables.py                  | 26 ++++++
 .../test => autotest}/test_fixtures.py        | 13 +--
 autotest/test_markers.py                      | 59 +++++++++++++
 .../test => autotest}/test_misc.py            | 35 ++------
 .../test => autotest}/test_ostags.py          |  1 +
 .../test => autotest}/test_zip.py             | 82 ++++++++-----------
 docs/md/executables.md                        | 11 ---
 docs/md/markers.md                            |  9 +-
 modflow_devtools/download.py                  |  2 +-
 modflow_devtools/executables.py               | 17 +---
 modflow_devtools/markers.py                   | 44 +++++++++-
 modflow_devtools/misc.py                      |  5 +-
 modflow_devtools/test/test_executables.py     | 44 ----------
 modflow_devtools/test/test_markers.py         | 49 -----------
 pyproject.toml                                |  8 +-
 23 files changed, 206 insertions(+), 242 deletions(-)
 rename {modflow_devtools/test => autotest}/__init__.py (100%)
 rename conftest.py => autotest/conftest.py (100%)
 rename pytest.ini => autotest/pytest.ini (72%)
 rename {modflow_devtools/test => autotest}/test_build.py (99%)
 rename {modflow_devtools/test => autotest}/test_download.py (99%)
 create mode 100644 autotest/test_executables.py
 rename {modflow_devtools/test => autotest}/test_fixtures.py (97%)
 create mode 100644 autotest/test_markers.py
 rename {modflow_devtools/test => autotest}/test_misc.py (90%)
 rename {modflow_devtools/test => autotest}/test_ostags.py (99%)
 rename {modflow_devtools/test => autotest}/test_zip.py (67%)
 delete mode 100644 modflow_devtools/test/test_executables.py
 delete mode 100644 modflow_devtools/test/test_markers.py

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9ca7cb0..dd5a40c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -80,24 +80,24 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-22.04, macos-12, windows-2022 ]
-        python: [ 3.8, 3.9, "3.10", "3.11" ]
+        python: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
     env:
       GCC_V: 11
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: modflow-devtools
       
       - name: Checkout modflow6
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: MODFLOW-USGS/modflow6
           path: modflow6
       
       - name: Checkout modflow6 examples
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: MODFLOW-USGS/modflow6-examples
           path: modflow6-examples
@@ -113,7 +113,6 @@ jobs:
         with:
           repository: MODFLOW-USGS/modflow6-largetestmodels
           path: modflow6-largetestmodels
-          token: ${{ github.token }}
 
       - name: Install executables
         uses: modflowpy/install-modflow-action@v1
@@ -128,10 +127,6 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
-          cache: 'pip'
-          cache-dependency-path: |
-            modflow-devtools/pyproject.toml
-            modflow6-examples/etc/requirements*.txt
 
       - name: Install Python packages
         working-directory: modflow-devtools
@@ -159,22 +154,19 @@ jobs:
         run: python ci_build_files.py
 
       - name: Run local tests
-        working-directory: modflow-devtools
+        working-directory: modflow-devtools/autotest
         env:
-          BIN_PATH: ~/.local/bin/modflow
           REPOS_PATH: ${{ github.workspace }}
-          GITHUB_TOKEN: ${{ github.token }}
         # use --dist loadfile to so tests requiring pytest-virtualenv run on the same worker
-        run: pytest -v -n auto --dist loadfile --durations 0 --ignore modflow_devtools/test/test_download.py
+        run: pytest -v -n auto --dist loadfile --durations 0 --ignore test_download.py
       
       - name: Run network-dependent tests
         # only invoke the GH API on one OS and Python version
         # to avoid rate limits (1000 rqs / hour / repository)
         # https://docs.github.com/en/actions/learn-github-actions/usage-limits-billing-and-administration#usage-limits
         if: runner.os == 'Linux' && matrix.python == '3.8'
-        working-directory: modflow-devtools
+        working-directory: modflow-devtools/autotest
         env:
-          BIN_PATH: ~/.local/bin/modflow
           REPOS_PATH: ${{ github.workspace }}
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v -n auto --durations 0 modflow_devtools/test/test_download.py
\ No newline at end of file
+        run: pytest -v -n auto --durations 0 test_download.py
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 4ad02b9..20eb2ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -128,8 +128,9 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# pycharme
+# IDEs
 .idea/
+.vscode/
 
 # downloaded exe
 modflow_devtools/bin/
diff --git a/DEVELOPER.md b/DEVELOPER.md
index b074df5..499e1b8 100644
--- a/DEVELOPER.md
+++ b/DEVELOPER.md
@@ -38,25 +38,21 @@ This repository's tests use [`pytest`](https://docs.pytest.org/en/latest/) and s
 
 This repository's tests expect a few environment variables:
 
-- `BIN_PATH`: path to MODFLOW 6 and related executables
 - `REPOS_PATH`: the path to MODFLOW 6 example model repositories
 - `GITHUB_TOKEN`: a GitHub authentication token
 
 These may be set manually, but the recommended approach is to configure environment variables in a `.env` file in the project root, for instance:
 
 ```
-BIN_PATH=/path/to/modflow/executables
 REPOS_PATH=/path/to/repos
 GITHUB_TOKEN=yourtoken...
 ```
 
 The tests use [`pytest-dotenv`](https://github.com/quiqua/pytest-dotenv) to detect and load variables from this file.
 
-**Note:** at minimum, the tests require that the `mf6` (or `mf6.exe` on Windows) executable is present in `BIN_PATH`.
-
 ### Running the tests
 
-Tests should be run from the project root. To run the tests in parallel with verbose output:
+Tests should be run from the `autotest` directory. To run the tests in parallel with verbose output:
 
 ```shell
 pytest -v -n auto
@@ -64,11 +60,11 @@ pytest -v -n auto
 
 ### Writing new tests
 
-Tests should follow a few conventions for ease of use and maintenance.
+Tests follow a few conventions for ease of use and maintenance.
 
 #### Temporary directories
 
-Tests which must write to disk should use `pytest`'s built-in `temp_dir` fixture or one of this package's own scoped temporary directory fixtures.
+Tests which must write to disk use `pytest`'s built-in `temp_dir` fixture or one of this package's own scoped temporary directory fixtures.
 
 ## Releasing
 
diff --git a/modflow_devtools/test/__init__.py b/autotest/__init__.py
similarity index 100%
rename from modflow_devtools/test/__init__.py
rename to autotest/__init__.py
diff --git a/conftest.py b/autotest/conftest.py
similarity index 100%
rename from conftest.py
rename to autotest/conftest.py
diff --git a/pytest.ini b/autotest/pytest.ini
similarity index 72%
rename from pytest.ini
rename to autotest/pytest.ini
index 93b6f6d..73fd077 100644
--- a/pytest.ini
+++ b/autotest/pytest.ini
@@ -4,5 +4,5 @@ python_files =
     test_*.py
     *_test*.py
 markers =
-    slow: tests that don't complete in a few seconds
+    slow: tests not completing in a few seconds
     meta: run by other tests (e.g. testing fixtures)
\ No newline at end of file
diff --git a/modflow_devtools/test/test_build.py b/autotest/test_build.py
similarity index 99%
rename from modflow_devtools/test/test_build.py
rename to autotest/test_build.py
index 3966ec0..36697f7 100644
--- a/modflow_devtools/test/test_build.py
+++ b/autotest/test_build.py
@@ -3,6 +3,7 @@
 from pathlib import Path
 
 import pytest
+
 from modflow_devtools.build import meson_build
 from modflow_devtools.markers import requires_pkg
 
diff --git a/modflow_devtools/test/test_download.py b/autotest/test_download.py
similarity index 99%
rename from modflow_devtools/test/test_download.py
rename to autotest/test_download.py
index 9fbfff7..9d5173d 100644
--- a/modflow_devtools/test/test_download.py
+++ b/autotest/test_download.py
@@ -1,5 +1,6 @@
 import pytest
 from flaky import flaky
+
 from modflow_devtools.download import (
     download_and_unzip,
     download_artifact,
diff --git a/autotest/test_executables.py b/autotest/test_executables.py
new file mode 100644
index 0000000..7d55a27
--- /dev/null
+++ b/autotest/test_executables.py
@@ -0,0 +1,26 @@
+import subprocess
+import sys
+from pathlib import Path
+from shutil import which
+
+import pytest
+
+from modflow_devtools.executables import Executables
+from modflow_devtools.misc import add_sys_path, get_suffixes
+
+ext, _ = get_suffixes(sys.platform)
+exe_stem = "pytest"
+exe_path = Path(which(exe_stem))
+bin_path = exe_path.parent
+exe = f"{exe_stem}{ext}"
+
+
+@pytest.fixture
+def exes():
+    with add_sys_path(bin_path):
+        yield Executables(**{exe_stem: bin_path / exe})
+
+
+def test_access(exes):
+    # support both attribute and dictionary style access
+    assert exes.pytest == exes["pytest"] == exe_path
diff --git a/modflow_devtools/test/test_fixtures.py b/autotest/test_fixtures.py
similarity index 97%
rename from modflow_devtools/test/test_fixtures.py
rename to autotest/test_fixtures.py
index 32d0f46..f959d0c 100644
--- a/modflow_devtools/test/test_fixtures.py
+++ b/autotest/test_fixtures.py
@@ -139,7 +139,7 @@ def test_keep_class_scoped_tmpdir(tmp_path, arg):
         TestKeepClassScopedTmpdirInner.test_keep_class_scoped_tmpdir_inner.__name__,
         "-M",
         "test_keep",
-        "-K",
+        arg,
         tmp_path,
     ]
     assert pytest.main(args) == ExitCode.OK
@@ -160,19 +160,14 @@ def test_keep_module_scoped_tmpdir(tmp_path, arg):
         test_keep_module_scoped_tmpdir_inner.__name__,
         "-M",
         "test_keep",
-        "-K",
+        arg,
         tmp_path,
     ]
     assert pytest.main(args) == ExitCode.OK
     this_path = Path(__file__)
     keep_path = (
-        tmp_path
-        / f"{str(this_path.parent.parent.name)}.{str(this_path.parent.name)}.{str(this_path.stem)}0"
+        tmp_path / f"{str(this_path.parent.name)}.{str(this_path.stem)}0"
     )
-    from pprint import pprint
-
-    print(keep_path)
-    pprint(list(keep_path.glob("*")))
     assert test_keep_fname in [f.name for f in keep_path.glob("*")]
 
 
@@ -186,7 +181,7 @@ def test_keep_session_scoped_tmpdir(tmp_path, arg, request):
         test_keep_session_scoped_tmpdir_inner.__name__,
         "-M",
         "test_keep",
-        "-K",
+        arg,
         tmp_path,
     ]
     assert pytest.main(args) == ExitCode.OK
diff --git a/autotest/test_markers.py b/autotest/test_markers.py
new file mode 100644
index 0000000..cd105c4
--- /dev/null
+++ b/autotest/test_markers.py
@@ -0,0 +1,59 @@
+from os import environ
+from platform import python_version, system
+from shutil import which
+
+from packaging.version import Version
+
+from modflow_devtools.markers import *
+
+exe = "pytest"
+
+
+@requires_exe(exe)
+def test_require_exe():
+    assert which(exe)
+    require_exe(exe)
+    require_program(exe)
+
+
+exes = [exe, "python"]
+
+
+@require_exe(*exes)
+def test_require_exe_multiple():
+    assert all(which(exe) for exe in exes)
+
+
+@requires_pkg("pytest")
+def test_requires_pkg():
+    import numpy
+
+    assert numpy is not None
+
+
+@requires_pkg("pytest", "pluggy")
+def test_requires_pkg_multiple():
+    import pluggy
+    import pytest
+
+    assert pluggy is not None and pytest is not None
+
+
+@requires_platform("Windows")
+def test_requires_platform():
+    assert system() == "Windows"
+
+
+@excludes_platform("Darwin", ci_only=True)
+def test_requires_platform_ci_only():
+    if "CI" in environ:
+        assert system() != "Darwin"
+
+
+py_ver = python_version()
+
+
+@pytest.mark.parametrize("version", ["3.12", "3.11"])
+def test_requires_python(version):
+    if Version(py_ver) >= Version(version):
+        assert requires_python(version)
diff --git a/modflow_devtools/test/test_misc.py b/autotest/test_misc.py
similarity index 90%
rename from modflow_devtools/test/test_misc.py
rename to autotest/test_misc.py
index ff4f980..7b65641 100644
--- a/modflow_devtools/test/test_misc.py
+++ b/autotest/test_misc.py
@@ -7,12 +7,13 @@
 from typing import List
 
 import pytest
-from conftest import project_root_path
+
 from modflow_devtools.misc import (
     get_model_paths,
     get_namefile_paths,
     get_packages,
     has_package,
+    has_pkg,
     set_dir,
     set_env,
     timed,
@@ -255,35 +256,9 @@ def test_get_namefile_paths_select_packages():
     assert len(paths) >= 43
 
 
-@pytest.mark.slow
-def test_has_pkg(virtualenv):
-    python = virtualenv.python
-    venv = Path(python).parent
-    pkg = "pytest"
-    dep = "pluggy"
-    print(
-        f"Using temp venv at {venv} with python {python} to test has_pkg('{pkg}') with and without '{dep}'"
-    )
-
-    # install a package and remove one of its dependencies
-    virtualenv.run(f"pip install {project_root_path}")
-    virtualenv.run(f"pip install {pkg}")
-    virtualenv.run(f"pip uninstall -y {dep}")
-
-    # check with/without strict mode
-    for strict in [False, True]:
-        cmd = (
-            f"from modflow_devtools.misc import has_pkg; print(has_pkg('{pkg}'"
-            + (", strict=True))" if strict else "))")
-        )
-        exp = "False" if strict else "True"
-        assert (
-            virtualenv.run(
-                f'{python} -c "{cmd}"',
-                capture=True,
-            ).strip()
-            == exp
-        )
+def test_has_pkg():
+    assert has_pkg("pytest")
+    assert not has_pkg("notapkg")
 
 
 def test_timed1(capfd):
diff --git a/modflow_devtools/test/test_ostags.py b/autotest/test_ostags.py
similarity index 99%
rename from modflow_devtools/test/test_ostags.py
rename to autotest/test_ostags.py
index 7ad3b91..22e93f1 100644
--- a/modflow_devtools/test/test_ostags.py
+++ b/autotest/test_ostags.py
@@ -1,6 +1,7 @@
 from platform import system
 
 import pytest
+
 from modflow_devtools.ostags import (
     OSTag,
     get_binary_suffixes,
diff --git a/modflow_devtools/test/test_zip.py b/autotest/test_zip.py
similarity index 67%
rename from modflow_devtools/test/test_zip.py
rename to autotest/test_zip.py
index b1aa28a..070b9c4 100644
--- a/modflow_devtools/test/test_zip.py
+++ b/autotest/test_zip.py
@@ -2,91 +2,73 @@
 import shutil
 import sys
 import zipfile
-from os import environ
 from pathlib import Path
 from pprint import pprint
+from shutil import which
 from zipfile import ZipFile
 
 import pytest
+
 from modflow_devtools.markers import excludes_platform
 from modflow_devtools.misc import get_suffixes, set_dir
 from modflow_devtools.zip import MFZipFile
 
-_bin_path = Path(environ.get("BIN_PATH")).expanduser().absolute()
-_ext, _ = get_suffixes(sys.platform)
-
-
-@pytest.fixture(scope="module")
-def empty_archive(module_tmpdir) -> Path:
-    # https://stackoverflow.com/a/25195628/6514033
-    data = b"PK\x05\x06\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00"
-    path = module_tmpdir / "empty.zip"
-
-    with open(path, "wb") as zip:
-        zip.write(data)
-
-    return path
-
-
-@pytest.fixture(scope="module")
-def nonempty_archive(module_tmpdir) -> Path:
-    if not _bin_path.is_dir():
-        pytest.skip(f"BIN_PATH ({_bin_path}) is not a directory")
-
-    zip_path = module_tmpdir / "nonempty.zip"
-    txt_path = module_tmpdir / "hw.txt"
-    exe_path = _bin_path / f"mf6{_ext}"
-
-    # create a zip file with a text file and an executable
-    shutil.copy(exe_path, module_tmpdir)
-    with open(txt_path, "w") as f:
-        f.write("hello world")
-
-    with set_dir(module_tmpdir):
-        zip = MFZipFile(zip_path.name, "w")
-        zip.write(txt_path.name, compress_type=zipfile.ZIP_DEFLATED)
-        zip.write(exe_path.name, compress_type=zipfile.ZIP_DEFLATED)
-        zip.close()
-
-    return zip_path
+ext, _ = get_suffixes(sys.platform)
+exe_stem = "pytest"
+exe_path = Path(which(exe_stem))
+exe_name = f"{exe_stem}{ext}"
 
 
 def test_compressall(function_tmpdir):
     zip_file = function_tmpdir / "output.zip"
     input_dir = function_tmpdir / "input"
     input_dir.mkdir()
-
     with open(input_dir / "data.txt", "w") as f:
         f.write("hello world")
 
     MFZipFile.compressall(str(zip_file), dir_pths=str(input_dir))
-
     pprint(list(function_tmpdir.iterdir()))
     assert zip_file.exists()
 
     output_dir = function_tmpdir / "output"
     output_dir.mkdir()
-
     ZipFile(zip_file).extractall(path=str(output_dir))
-
     pprint(list(output_dir.iterdir()))
     assert (output_dir / "data.txt").is_file()
 
 
+@pytest.fixture(scope="module")
+def empty_archive(module_tmpdir) -> Path:
+    # https://stackoverflow.com/a/25195628/6514033
+    data = b"PK\x05\x06\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00"
+    path = module_tmpdir / "empty.zip"
+    with open(path, "wb") as zip:
+        zip.write(data)
+    yield path
+
+
 def test_extractall_empty(empty_archive, function_tmpdir):
     zf = MFZipFile(empty_archive, "r")
     zf.extractall(str(function_tmpdir))
-
     assert not any(function_tmpdir.iterdir())
 
 
+@pytest.fixture(scope="module")
+def archive(module_tmpdir) -> Path:
+    zip_path = module_tmpdir / "nonempty.zip"
+    shutil.copy(exe_path, module_tmpdir)
+    with set_dir(module_tmpdir):
+        zip = MFZipFile(zip_path.name, "w")
+        zip.write(exe_path.name, compress_type=zipfile.ZIP_DEFLATED)
+        zip.close()
+    yield zip_path
+
+
 @pytest.mark.parametrize("mf", [True, False])
 @excludes_platform("Windows")
-def test_preserves_execute_permission(function_tmpdir, nonempty_archive, mf):
-    zip = MFZipFile(nonempty_archive) if mf else ZipFile(nonempty_archive)
+def test_extractall_preserves_execute_permission(function_tmpdir, archive, mf):
+    zip = MFZipFile(archive) if mf else ZipFile(archive)
     zip.extractall(path=str(function_tmpdir))
-
-    exe_path = function_tmpdir / f"mf6{_ext}"
-
-    assert exe_path.is_file()
-    assert os.access(exe_path, os.X_OK) == mf
+    path = function_tmpdir / exe_name
+    assert path.is_file()
+    assert os.access(path, os.X_OK) == mf
diff --git a/docs/md/executables.md b/docs/md/executables.md
index d235cc5..cfc8d79 100644
--- a/docs/md/executables.md
+++ b/docs/md/executables.md
@@ -29,14 +29,3 @@ def test_targets(targets):
     # attribute- and dictionary-style access is supported
     assert targets["mf6"] == targets.mf6
 ```
-
-There is also a convenience function for getting a program's version string. The function will automatically strip the program name from the output (assumed delimited with `:`).
-
-```python
-import subprocess
-
-def test_executables_version(targets):
-    # returns e.g. '6.4.1 Release 12/09/2022'
-    assert targets.get_version(targets.mf6) == \  
-           subprocess.check_output([f"{targets.mf6}", "-v"]).decode('utf-8').strip().split(":")[1].strip()
-```
diff --git a/docs/md/markers.md b/docs/md/markers.md
index bd9714c..a50aec3 100644
--- a/docs/md/markers.md
+++ b/docs/md/markers.md
@@ -78,4 +78,11 @@ Both these markers accept a `ci_only` flag, which indicates whether the policy s
 Markers are also provided to ping network resources and skip if unavailable:
 
 - `@requires_github`: skips if `github.com` is unreachable
-- `@requires_spatial_reference`: skips if `spatialreference.org` is unreachable
\ No newline at end of file
+- `@requires_spatial_reference`: skips if `spatialreference.org` is unreachable
+
+## Aliases
+
+All markers are aliased to imperative mood, e.g. `require_github`. Some have other aliases as well:
+
+`requires_pkg` -> `require[s]_package`
+`requires_exe` -> `require[s]_program`
diff --git a/modflow_devtools/download.py b/modflow_devtools/download.py
index 3741f05..fcf045b 100644
--- a/modflow_devtools/download.py
+++ b/modflow_devtools/download.py
@@ -87,7 +87,7 @@ def get_response_json():
                     return json.loads(resp.read().decode())
             except urllib.error.HTTPError as err:
                 if err.code == 401 and os.environ.get("GITHUB_TOKEN"):
-                    raise ValueError("GITHUB_TOKEN env is invalid") from err
+                    raise ValueError("GITHUB_TOKEN is invalid") from err
                 elif err.code == 403 and "rate limit exceeded" in err.reason:
                     raise ValueError(
                         f"use GITHUB_TOKEN env to bypass rate limit ({err})"
diff --git a/modflow_devtools/executables.py b/modflow_devtools/executables.py
index 28c966d..9ec0370 100644
--- a/modflow_devtools/executables.py
+++ b/modflow_devtools/executables.py
@@ -1,10 +1,6 @@
-import sys
-from os import PathLike
 from pathlib import Path
 from types import SimpleNamespace
-from typing import Dict, Optional
-
-from modflow_devtools.misc import get_suffixes, run_cmd
+from typing import Dict
 
 
 class Executables(SimpleNamespace):
@@ -27,14 +23,3 @@ def as_dict(self) -> Dict[str, Path]:
         """
 
         return self.__dict__.copy()
-
-    @staticmethod
-    def get_version(path: PathLike = None, flag: str = "-v") -> Optional[str]:
-        """Get an executable's version string."""
-
-        out, err, ret = run_cmd(str(path), flag)
-        if ret == 0:
-            out = "".join(out).strip()
-            return out.split(":")[1].strip()
-        else:
-            return None
diff --git a/modflow_devtools/markers.py b/modflow_devtools/markers.py
index d40ca5c..1c21e43 100644
--- a/modflow_devtools/markers.py
+++ b/modflow_devtools/markers.py
@@ -1,4 +1,11 @@
-from platform import system
+"""
+Pytest markers to toggle tests based on environment conditions.
+Occasionally useful to directly assert environment expectations.
+"""
+
+from platform import python_version, system
+
+from packaging.version import Version
 
 from modflow_devtools.imports import import_optional_dependency
 from modflow_devtools.misc import (
@@ -10,6 +17,7 @@
 )
 
 pytest = import_optional_dependency("pytest")
+py_ver = Version(python_version())
 
 
 def requires_exe(*exes):
@@ -21,6 +29,23 @@ def requires_exe(*exes):
     )
 
 
+def requires_python(version, bound="lower"):
+    if not isinstance(version, str):
+        raise ValueError(f"Version must a string")
+
+    py_tgt = Version(version)
+    if bound == "lower":
+        return py_ver >= py_tgt
+    elif bound == "upper":
+        return py_ver <= py_tgt
+    elif bound == "exact":
+        return py_ver == py_tgt
+    else:
+        return ValueError(
+            f"Invalid bound type: {bound} (use 'upper', 'lower', or 'exact')"
+        )
+
+
 def requires_pkg(*pkgs):
     missing = {pkg for pkg in pkgs if not has_pkg(pkg, strict=True)}
     return pytest.mark.skipif(
@@ -69,3 +94,20 @@ def excludes_branch(branch):
     not is_connected("spatialreference.org"),
     reason="spatialreference.org is required.",
 )
+
+
+# imperative mood renaming, and some aliases
+
+require_exe = requires_exe
+require_program = requires_exe
+requires_program = requires_exe
+require_python = requires_python
+require_pkg = requires_pkg
+require_package = requires_pkg
+requires_package = requires_pkg
+require_platform = requires_platform
+exclude_platform = excludes_platform
+require_branch = requires_branch
+exclude_branch = excludes_branch
+require_github = requires_github
+require_spatial_reference = requires_spatial_reference
diff --git a/modflow_devtools/misc.py b/modflow_devtools/misc.py
index 9646aee..4915d8c 100644
--- a/modflow_devtools/misc.py
+++ b/modflow_devtools/misc.py
@@ -66,8 +66,9 @@ def set_env(*remove, **update):
 
 class add_sys_path:
     """
-    Context manager for temporarily editing the system path
-    (https://stackoverflow.com/a/39855753/6514033)
+    Context manager to add temporarily to the system path.
+
+    Adapted from https://stackoverflow.com/a/39855753/6514033.
     """
 
     def __init__(self, path):
diff --git a/modflow_devtools/test/test_executables.py b/modflow_devtools/test/test_executables.py
deleted file mode 100644
index 483103a..0000000
--- a/modflow_devtools/test/test_executables.py
+++ /dev/null
@@ -1,44 +0,0 @@
-import subprocess
-import sys
-from os import environ
-from pathlib import Path
-
-import pytest
-from modflow_devtools.executables import Executables
-from modflow_devtools.misc import add_sys_path, get_suffixes
-
-_bin_path = Path(environ.get("BIN_PATH")).expanduser().absolute()
-_ext, _ = get_suffixes(sys.platform)
-
-
-@pytest.fixture
-def exes():
-    if not _bin_path.is_dir():
-        pytest.skip(f"BIN_PATH ({_bin_path}) is not a directory")
-
-    with add_sys_path(str(_bin_path)):
-        yield Executables(
-            **{
-                "mf6": _bin_path / f"mf6{_ext}",
-            }
-        )
-
-
-def test_get_version(exes):
-    ver_str = Executables.get_version(exes.mf6)
-    version = (
-        subprocess.check_output([f"{exes.mf6}", "-v"])
-        .decode("utf-8")
-        .split(":")[1]
-        .strip()
-    )
-    assert ver_str == version
-    assert int(ver_str[0].split(".")[0]) >= 6
-
-
-def test_mapping(exes):
-    print(exes.mf6)
-    assert (
-        exes.mf6 == exes["mf6"]
-    )  # should support both attribute and dictionary access
-    assert exes.mf6 == _bin_path / f"mf6{_ext}"  # should be the correct path
diff --git a/modflow_devtools/test/test_markers.py b/modflow_devtools/test/test_markers.py
deleted file mode 100644
index 95f497c..0000000
--- a/modflow_devtools/test/test_markers.py
+++ /dev/null
@@ -1,49 +0,0 @@
-from os import environ
-from platform import system
-from shutil import which
-
-from modflow_devtools.markers import (
-    excludes_platform,
-    requires_exe,
-    requires_pkg,
-    requires_platform,
-)
-
-
-@requires_exe("mf6")
-def test_requires_exe():
-    assert which("mf6")
-
-
-exes = ["mfusg", "mfnwt"]
-
-
-@requires_exe(*exes)
-def test_requires_exe_multiple():
-    assert all(which(exe) for exe in exes)
-
-
-@requires_pkg("numpy")
-def test_requires_pkg():
-    import numpy
-
-    assert numpy is not None
-
-
-@requires_pkg("numpy", "matplotlib")
-def test_requires_pkg_multiple():
-    import matplotlib
-    import numpy
-
-    assert numpy is not None and matplotlib is not None
-
-
-@requires_platform("Windows")
-def test_requires_platform():
-    assert system() == "Windows"
-
-
-@excludes_platform("Darwin", ci_only=True)
-def test_requires_platform_ci_only():
-    if "CI" in environ:
-        assert system() != "Darwin"
diff --git a/pyproject.toml b/pyproject.toml
index c3630b7..4d2a701 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,6 +10,9 @@ name = "modflow-devtools"
 description = "Python tools for MODFLOW development"
 authors = [
     {name = "Joseph D. Hughes", email = "modflow@usgs.gov"},
+    {name = "Michael Reno", email = "mreno@ucar.edu"},
+    {name = "Mike Taves", email = "mwtoews@gmail.com"},
+    {name = "Wes Bonelli", email = "wbonelli@ucar.edu"},
 ]
 maintainers = [
     {name = "Joseph D. Hughes", email = "modflow@usgs.gov"},
@@ -33,6 +36,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Hydrology"
 ]
 requires-python = ">=3.8"
@@ -58,7 +62,6 @@ test = [
     "pytest-cases",
     "pytest-cov",
     "pytest-dotenv",
-    "pytest-virtualenv",
     "pytest-xdist",
     "PyYaml"
 ]
@@ -84,10 +87,11 @@ verbose = true
 
 [tool.isort]
 profile = "black"
-src_paths = ["src/modflow_devtools"]
+src_paths = ["modflow_devtools"]
 line_length = 79
 
 [tool.setuptools]
+packages = ["modflow_devtools"]
 include-package-data = true
 zip-safe = false
 

From 5b61a4b393b0bcd40aafeb87d1e80b3e557e0f05 Mon Sep 17 00:00:00 2001
From: wpbonelli <wbonelli@ucar.edu>
Date: Tue, 21 Nov 2023 10:36:35 -0500
Subject: [PATCH 11/12] feat(executables): support .get(key, default) like dict
 (#125)

---
 autotest/test_executables.py    | 4 +++-
 docs/md/executables.md          | 2 ++
 modflow_devtools/executables.py | 3 +++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/autotest/test_executables.py b/autotest/test_executables.py
index 7d55a27..c06edc3 100644
--- a/autotest/test_executables.py
+++ b/autotest/test_executables.py
@@ -1,4 +1,3 @@
-import subprocess
 import sys
 from pathlib import Path
 from shutil import which
@@ -24,3 +23,6 @@ def exes():
 def test_access(exes):
     # support both attribute and dictionary style access
     assert exes.pytest == exes["pytest"] == exe_path
+    # .get() works too
+    assert exes.get("not a target") is None
+    assert exes.get("not a target", exes["pytest"]) == exes["pytest"]
diff --git a/docs/md/executables.md b/docs/md/executables.md
index cfc8d79..ef1085f 100644
--- a/docs/md/executables.md
+++ b/docs/md/executables.md
@@ -28,4 +28,6 @@ The `targets` fixture can then be injected into test functions:
 def test_targets(targets):
     # attribute- and dictionary-style access is supported
     assert targets["mf6"] == targets.mf6
+    # .get() works too
+    assert targets.get("not a target") is None
 ```
diff --git a/modflow_devtools/executables.py b/modflow_devtools/executables.py
index 9ec0370..0c9705e 100644
--- a/modflow_devtools/executables.py
+++ b/modflow_devtools/executables.py
@@ -17,6 +17,9 @@ def __setitem__(self, key, item):
     def __getitem__(self, key):
         return self.__dict__[key]
 
+    def get(self, key, default=None):
+        return self.as_dict().get(key, default)
+
     def as_dict(self) -> Dict[str, Path]:
         """
         Returns a dictionary mapping executable names to paths.

From 4be45b28b2334c3a3dee5a307758c9586ce4f6fd Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 21 Nov 2023 15:39:08 +0000
Subject: [PATCH 12/12] ci(release): set version to 1.3.0, update changelog

---
 HISTORY.md                   | 12 ++++++++++++
 docs/conf.py                 |  2 +-
 modflow_devtools/__init__.py |  4 ++--
 version.txt                  |  2 +-
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/HISTORY.md b/HISTORY.md
index 0f7d8d9..de0e5cb 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,3 +1,15 @@
+### Version 1.3.0
+
+#### New features
+
+* [feat(fixtures)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/0ce571411b6b35bc62d4f333d1a961bd2f202784): Add --tabular pytest CLI arg and corresponding fixture (#116). Committed by wpbonelli on 2023-09-12.
+* [feat(timeit)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/506a238f6f31d827015a6c6f5ba1867ee55948a7): Add function timing decorator (#118). Committed by wpbonelli on 2023-09-12.
+* [feat(executables)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/5b61a4b393b0bcd40aafeb87d1e80b3e557e0f05): Support .get(key, default) like dict (#125). Committed by wpbonelli on 2023-11-21.
+
+#### Refactoring
+
+* [refactor](https://github.com/MODFLOW-USGS/modflow-devtools/commit/cd644fa90885cde04f36f24e44cfe922b2a38897): Support python 3.12, various updates (#124). Committed by wpbonelli on 2023-11-11.
+
 ### Version 1.2.0
 
 #### New features
diff --git a/docs/conf.py b/docs/conf.py
index 5b64ea9..aa50e63 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -8,7 +8,7 @@
 
 project = "modflow-devtools"
 author = "MODFLOW Team"
-release = "1.3.0.dev0"
+release = "1.3.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/modflow_devtools/__init__.py b/modflow_devtools/__init__.py
index 436d4e8..be89f8f 100644
--- a/modflow_devtools/__init__.py
+++ b/modflow_devtools/__init__.py
@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
-__date__ = "Sep 12, 2023"
-__version__ = "1.3.0.dev0"
+__date__ = "Nov 21, 2023"
+__version__ = "1.3.0"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "jdhughes@usgs.gov"
 __status__ = "Production"
diff --git a/version.txt b/version.txt
index 14c65ab..589268e 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-1.3.0.dev0
\ No newline at end of file
+1.3.0
\ No newline at end of file