From 4a7adc0edcb265871fdb805d6edb0df3d49693c2 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Sat, 5 Aug 2023 18:12:37 +0000
Subject: [PATCH 1/4] ci(release): update to development version 1.1.0.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 0048764..f780c20 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -8,7 +8,7 @@
 
 project = "modflow-devtools"
 author = "MODFLOW Team"
-release = "1.0.0"
+release = "1.1.0.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 ea1d042..a825793 100644
--- a/modflow_devtools/__init__.py
+++ b/modflow_devtools/__init__.py
@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
 __date__ = "Aug 05, 2023"
-__version__ = "1.0.0"
+__version__ = "1.1.0.dev0"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "jdhughes@usgs.gov"
 __status__ = "Production"
diff --git a/version.txt b/version.txt
index afaf360..64b95b0 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-1.0.0
\ No newline at end of file
+1.1.0.dev0
\ No newline at end of file

From 582d48a4d72f18a787216ada5befb7543cebdfcf Mon Sep 17 00:00:00 2001
From: w-bonelli <wbonelli@ucar.edu>
Date: Tue, 8 Aug 2023 01:31:23 -0400
Subject: [PATCH 2/4] refactor: deprecate misc functions, add ostags
 alternatives (#105)

- deprecate misc.get_ostag() for ostags.get_modflow_ostag()
- deprecate misc.get_suffixes() for ostags.get_binary_suffixes()
- improve some docstrings
- expand tests
- update docs
---
 docs/md/ostags.md                    | 11 +++++++
 modflow_devtools/misc.py             | 47 ++++++++++++++++++++++++----
 modflow_devtools/ostags.py           | 46 +++++++++++++++++++++++++--
 modflow_devtools/test/test_ostags.py | 41 +++++++++++++++++++++++-
 4 files changed, 135 insertions(+), 10 deletions(-)

diff --git a/docs/md/ostags.md b/docs/md/ostags.md
index e140d98..ea9440c 100644
--- a/docs/md/ostags.md
+++ b/docs/md/ostags.md
@@ -43,3 +43,14 @@ OSTag.convert(platform.system(), "py2mf")
 The second argument specifies the mapping in format `<source>2<target>`, where `<source>` and `<target>` may take values `py`, `mf`, or `gh`.
 
 **Note**: source and target must be different.
+
+## 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.
+
+```python
+get_binary_suffixes()  # get extensions for current OS
+get_binary_suffixes("linux")  # returns ("", ".so")
+get_binary_suffixes("linux")  # returns ("", ".so")
+get_binary_suffixes("win64")  # returns (".exe", ".dll")
+```
diff --git a/modflow_devtools/misc.py b/modflow_devtools/misc.py
index c326c0b..31d540d 100644
--- a/modflow_devtools/misc.py
+++ b/modflow_devtools/misc.py
@@ -82,7 +82,12 @@ def __exit__(self, exc_type, exc_value, traceback):
 
 
 def get_ostag() -> str:
-    """Determine operating system tag from sys.platform."""
+    """
+    Determine operating system tag from sys.platform.
+
+    .. deprecated:: 1.1.0
+        Use ``ostags.get_modflow_ostag()`` instead.
+    """
     if sys.platform.startswith("linux"):
         return "linux"
     elif sys.platform.startswith("win"):
@@ -93,7 +98,12 @@ def get_ostag() -> str:
 
 
 def get_suffixes(ostag) -> Tuple[str, str]:
-    """Returns executable and library suffixes for the given OS (as returned by sys.platform)"""
+    """
+    Returns executable and library suffixes for the given OS (as returned by sys.platform)
+
+    .. deprecated:: 1.1.0
+        Use ``ostags.get_binary_suffixes()`` instead.
+    """
 
     tag = ostag.lower()
 
@@ -136,6 +146,23 @@ def run_py_script(script, *args, verbose=False):
 
 
 def get_current_branch() -> str:
+    """
+    Tries to determine the name of the current branch, first by the GITHUB_REF
+    environent variable, then by asking ``git`` if GITHUB_REF is not set.
+
+    Returns
+    -------
+    str
+        name of the current branch
+
+    Raises
+    ------
+    RuntimeError
+        if ``git`` is not available
+    ValueError
+        if the current branch could not be determined
+    """
+
     # check if on GitHub Actions CI
     ref = environ.get("GITHUB_REF")
     if ref is not None:
@@ -160,6 +187,7 @@ def get_packages(namefile_path: PathLike) -> List[str]:
     ----------
     namefile_path : PathLike
         path to MODFLOW 6 simulation or model name file
+
     Returns
     -------
         a list of packages used by the simulation or model
@@ -215,7 +243,9 @@ def parse_model_namefile(line):
 
 
 def has_package(namefile_path: PathLike, package: str) -> bool:
-    """Determines whether the model with the given namefile contains the selected package"""
+    """
+    Determines whether the model with the given namefile contains the selected package.
+    """
     packages = get_packages(namefile_path)
     return package.lower() in packages
 
@@ -306,7 +336,9 @@ def get_model_paths(
 def is_connected(hostname):
     """
     Tests whether the given URL is accessible.
-    See https://stackoverflow.com/a/20913928/."""
+    See https://stackoverflow.com/a/20913928/.
+    """
+
     try:
         host = socket.gethostbyname(hostname)
         s = socket.create_connection((host, 80), 2)
@@ -318,7 +350,10 @@ def is_connected(hostname):
 
 
 def is_in_ci():
-    """Determines whether the current process is running GitHub Actions CI"""
+    """
+    Determines whether the current process is running GitHub Actions CI
+    by checking for the "CI" environment variable.
+    """
 
     # if running in GitHub Actions CI, "CI" variable always set to true
     # https://docs.github.com/en/actions/learn-github-actions/environment-variables#default-environment-variables
@@ -328,7 +363,7 @@ def is_in_ci():
 def is_github_rate_limited() -> Optional[bool]:
     """
     Determines if a GitHub API rate limit is applied to the current IP.
-    Running this function will consume an API request!
+    Calling this function will consume an API request!
 
     Returns
     -------
diff --git a/modflow_devtools/ostags.py b/modflow_devtools/ostags.py
index 55e7706..3c68ed3 100644
--- a/modflow_devtools/ostags.py
+++ b/modflow_devtools/ostags.py
@@ -1,18 +1,20 @@
 """
-MODFLOW 6, Python3, and build servers may all refer to operating
-systems by different names. This module contains conversion utilities.
+MODFLOW 6, Python3, and GitHub Actions refer to operating
+systems differently. This module contains conversion utilities.
 """
 
 
+import sys
 from enum import Enum
 from platform import system
+from typing import Tuple
 
 _system = system()
 
 
 def get_modflow_ostag() -> str:
     if _system == "Windows":
-        return "win64"
+        return "win" + ("64" if sys.maxsize > 2**32 else "32")
     elif _system == "Linux":
         return "linux"
     elif _system == "Darwin":
@@ -30,6 +32,44 @@ def get_github_ostag() -> str:
         raise NotImplementedError(f"Unsupported system: {_system}")
 
 
+def get_binary_suffixes(ostag: str = None) -> Tuple[str, str]:
+    """
+    Returns executable and library suffixes for the given OS tag, if provided,
+    otherwise for the current operating system.
+
+    Parameters
+    ----------
+    ostag : str, optional
+        The OS tag. May be provided in modflow, python, or github format.
+
+    Returns
+    -------
+    Tuple[str, str]
+        The executable and library suffixes, respectively.
+    """
+
+    if ostag is None:
+        ostag = get_modflow_ostag()
+
+    def _suffixes(tag):
+        if tag in ["win32", "win64"]:
+            return ".exe", ".dll"
+        elif tag == "linux":
+            return "", ".so"
+        elif tag == "mac" or tag == "darwin":
+            return "", ".dylib"
+        else:
+            raise KeyError(f"unrecognized OS tag: {tag!r}")
+
+    try:
+        return _suffixes(ostag.lower())
+    except:
+        try:
+            return _suffixes(python_to_modflow_ostag(ostag))
+        except:
+            return _suffixes(github_to_modflow_ostag(ostag))
+
+
 def python_to_modflow_ostag(tag: str) -> str:
     """
     Convert a platform.system() string to an ostag as expected
diff --git a/modflow_devtools/test/test_ostags.py b/modflow_devtools/test/test_ostags.py
index 02d9adb..7ad3b91 100644
--- a/modflow_devtools/test/test_ostags.py
+++ b/modflow_devtools/test/test_ostags.py
@@ -1,7 +1,12 @@
 from platform import system
 
 import pytest
-from modflow_devtools.ostags import OSTag, get_github_ostag, get_modflow_ostag
+from modflow_devtools.ostags import (
+    OSTag,
+    get_binary_suffixes,
+    get_github_ostag,
+    get_modflow_ostag,
+)
 
 _system = system()
 
@@ -53,3 +58,37 @@ def test_get_github_ostag():
 )
 def test_ostag_convert(cvt, tag, exp):
     assert OSTag.convert(tag, cvt) == exp
+
+
+def test_get_binary_suffixes():
+    exe, lib = get_binary_suffixes()
+    if _system == "Windows":
+        assert exe == ".exe"
+        assert lib == ".dll"
+    elif _system == "Linux":
+        assert exe == ""
+        assert lib == ".so"
+    elif _system == "Darwin":
+        assert exe == ""
+        assert lib == ".dylib"
+
+
+@pytest.mark.parametrize(
+    "tag,exe,lib",
+    [
+        ("win64", ".exe", ".dll"),
+        ("win32", ".exe", ".dll"),
+        ("Windows", ".exe", ".dll"),
+        ("linux", "", ".so"),
+        ("Linux", "", ".so"),
+        ("mac", "", ".dylib"),
+        ("macOS", "", ".dylib"),
+        ("Darwin", "", ".dylib"),
+    ],
+)
+def test_get_binary_suffixes_given_tag(tag, exe, lib):
+    from modflow_devtools.misc import get_suffixes
+
+    assert get_binary_suffixes(tag) == (exe, lib)
+    if tag in ("win64", "win32", "linux", "mac"):
+        assert get_suffixes(tag) == (exe, lib)

From 03ea04157190480b455e174de64c692ff3bb86a3 Mon Sep 17 00:00:00 2001
From: w-bonelli <wbonelli@ucar.edu>
Date: Sat, 12 Aug 2023 12:47:03 -0400
Subject: [PATCH 3/4] refactor(has_pkg): introduce strict flag (#106)

* add strict flag to has_pkg() toggling whether to try to import or only check metadata
* always invalidate/refresh the installed package cache if strict is on
* add pytest-virtualenv to test dependencies, test with/without strict
* use --dist loadfile with xdist in CI for compatibility
* use strict=True for requires_pkg marker
---
 .github/workflows/ci.yml           |  3 ++-
 conftest.py                        |  3 +++
 modflow_devtools/markers.py        |  2 +-
 modflow_devtools/misc.py           | 42 ++++++++++++++++++++++++------
 modflow_devtools/test/test_misc.py | 34 ++++++++++++++++++++++++
 pyproject.toml                     |  1 +
 6 files changed, 75 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1c18594..4738d35 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -167,7 +167,8 @@ jobs:
           BIN_PATH: ~/.local/bin/modflow
           REPOS_PATH: ${{ github.workspace }}
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v -n auto --durations 0 --ignore modflow_devtools/test/test_download.py
+        # 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
       
       - name: Run network-dependent tests
         # only invoke the GH API on one OS and Python version
diff --git a/conftest.py b/conftest.py
index 74bcb56..d952441 100644
--- a/conftest.py
+++ b/conftest.py
@@ -1 +1,4 @@
+from pathlib import Path
+
 pytest_plugins = ["modflow_devtools.fixtures"]
+project_root_path = Path(__file__).parent
diff --git a/modflow_devtools/markers.py b/modflow_devtools/markers.py
index 0aa4b25..d40ca5c 100644
--- a/modflow_devtools/markers.py
+++ b/modflow_devtools/markers.py
@@ -22,7 +22,7 @@ def requires_exe(*exes):
 
 
 def requires_pkg(*pkgs):
-    missing = {pkg for pkg in pkgs if not has_pkg(pkg)}
+    missing = {pkg for pkg in pkgs if not has_pkg(pkg, strict=True)}
     return pytest.mark.skipif(
         missing,
         reason=f"missing package{'s' if len(missing) != 1 else ''}: "
diff --git a/modflow_devtools/misc.py b/modflow_devtools/misc.py
index 31d540d..7dd9210 100644
--- a/modflow_devtools/misc.py
+++ b/modflow_devtools/misc.py
@@ -398,21 +398,47 @@ def has_exe(exe):
     return _has_exe_cache[exe]
 
 
-def has_pkg(pkg):
+def has_pkg(pkg: str, strict: bool = False) -> bool:
     """
     Determines if the given Python package is installed.
 
+    Parameters
+    ----------
+    pkg : str
+        Name of the package to check.
+    strict : bool
+        If False, only check if package metadata is available.
+        If True, try to import the package (all dependencies must be present).
+
+    Returns
+    -------
+    bool
+        True if the package is installed, otherwise False.
+
+    Notes
+    -----
     Originally written by Mike Toews (mwtoews@gmail.com) for FloPy.
     """
-    if pkg not in _has_pkg_cache:
-        found = True
+
+    def try_import():
+        try:  # import name, e.g. "import shapefile"
+            importlib.import_module(pkg)
+            return True
+        except ModuleNotFoundError:
+            return False
+
+    def try_metadata() -> bool:
         try:  # package name, e.g. pyshp
             metadata.distribution(pkg)
+            return True
         except metadata.PackageNotFoundError:
-            try:  # import name, e.g. "import shapefile"
-                importlib.import_module(pkg)
-            except ModuleNotFoundError:
-                found = False
-        _has_pkg_cache[pkg] = found
+            return False
+
+    found = False
+    if not strict:
+        found = pkg in _has_pkg_cache or try_metadata()
+    if not found:
+        found = try_import()
+    _has_pkg_cache[pkg] = found
 
     return _has_pkg_cache[pkg]
diff --git a/modflow_devtools/test/test_misc.py b/modflow_devtools/test/test_misc.py
index fe6d2cb..79ea786 100644
--- a/modflow_devtools/test/test_misc.py
+++ b/modflow_devtools/test/test_misc.py
@@ -2,14 +2,17 @@
 import shutil
 from os import environ
 from pathlib import Path
+from pprint import pprint
 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,
 )
@@ -249,3 +252,34 @@ def test_get_namefile_paths_select_patterns():
 def test_get_namefile_paths_select_packages():
     paths = get_namefile_paths(_examples_path, packages=["wel"])
     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
+        )
diff --git a/pyproject.toml b/pyproject.toml
index 3dedbcb..c3630b7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,6 +58,7 @@ test = [
     "pytest-cases",
     "pytest-cov",
     "pytest-dotenv",
+    "pytest-virtualenv",
     "pytest-xdist",
     "PyYaml"
 ]

From cacd9440f1da56a7c09137532ec93757f12d2239 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Sat, 12 Aug 2023 16:51:11 +0000
Subject: [PATCH 4/4] ci(release): set version to 1.1.0, update changelog

---
 HISTORY.md                   | 7 +++++++
 docs/conf.py                 | 2 +-
 modflow_devtools/__init__.py | 4 ++--
 version.txt                  | 2 +-
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/HISTORY.md b/HISTORY.md
index 906d6a1..96524f3 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,3 +1,10 @@
+### Version 1.1.0
+
+#### Refactoring
+
+* [refactor](https://github.com/MODFLOW-USGS/modflow-devtools/commit/582d48a4d72f18a787216ada5befb7543cebdfcf): Deprecate misc functions, add ostags alternatives (#105). Committed by w-bonelli on 2023-08-08.
+* [refactor(has_pkg)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/03ea04157190480b455e174de64c692ff3bb86a3): Introduce strict flag (#106). Committed by w-bonelli on 2023-08-12.
+
 ### Version 1.0.0
 
 #### New features
diff --git a/docs/conf.py b/docs/conf.py
index f780c20..dbe6721 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -8,7 +8,7 @@
 
 project = "modflow-devtools"
 author = "MODFLOW Team"
-release = "1.1.0.dev0"
+release = "1.1.0"
 
 # -- 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 a825793..abd3212 100644
--- a/modflow_devtools/__init__.py
+++ b/modflow_devtools/__init__.py
@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
-__date__ = "Aug 05, 2023"
-__version__ = "1.1.0.dev0"
+__date__ = "Aug 12, 2023"
+__version__ = "1.1.0"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "jdhughes@usgs.gov"
 __status__ = "Production"
diff --git a/version.txt b/version.txt
index 64b95b0..1cc5f65 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-1.1.0.dev0
\ No newline at end of file
+1.1.0
\ No newline at end of file