Merge pull request #151 from marshall-lab/add-setup

Make titan installable

setup.py

@@ -0,0 +1,73 @@
+import setuptools
+import subprocess
+
+# ========= FROM https://github.com/vivin/better-setuptools-git-version/blob/master/better_setuptools_git_version.py with edits =========
+def get_latest_tag():
+    return subprocess.getoutput(
+        "git describe --tags `git rev-list --tags --max-count=1`"
+    )
+
+
+def get_tag_commit_sha(tag):
+    """Return the commit that the tag is pointing to."""
+    return subprocess.getoutput("git rev-list -n 1 {tag}".format(tag=tag))
+
+
+def get_head_sha():
+    """Return the sha key of HEAD."""
+    return subprocess.getoutput("git rev-parse HEAD")
+
+
+def is_head_at_tag(tag):
+    """Return True or False depending on whether the given tag is pointing to HEAD"""
+    return get_head_sha() == get_tag_commit_sha(tag)
+
+
+def get_version():
+    """
+    Return the full git version using the given template. If there are no annotated tags, the version specified by
+    starting_version will be used. If HEAD is at the tag, the version will be the tag itself. If there are commits ahead
+    of the tag, the first 8 characters of the sha of the HEAD commit will be included.
+    In all of the above cases, if the working tree is also dirty or contains untracked files, a "+dirty" suffix will be
+    appended to the version.
+    Returns:
+        the formatted version based on tags in the git repository.
+    """
+    template = "{tag}.dev{sha}"
+    tag = get_latest_tag()
+    if is_head_at_tag(tag):
+        version = tag
+    else:
+        sha = get_head_sha()[:8]
+        version = template.format(tag=tag, sha=sha)
+
+    return version
+
+
+# add the readme as the description
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+# make the requirements.txt be installed (not good practice for general packaging, good for current oscar set up)
+with open("requirements.txt") as f:
+    required = f.read().splitlines()
+
+setuptools.setup(
+    name="titan",  # Replace with your own username,
+    version=get_version(),
+    # author="Example Author",
+    # author_email="[email protected]",
+    description="TITAN Agent Based Model",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/marshall-lab/TITAN",
+    packages=setuptools.find_packages(),
+    install_requires=required,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+    ],
+    python_requires=">=3.6",
+    package_data={"titan": ["params/*.yml", "settings/*/*.yml"]},
+    entry_points={"console_scripts": ["run_titan=titan:script_init"]},
+)

tests/integration_test.py

@@ -30,7 +30,9 @@ def _make_model_integration():
 
 @pytest.mark.integration_deterministic
 def test_model_runs():
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
     )
@@ -39,11 +41,26 @@ def test_model_runs():
     assert True
 
 
+@pytest.mark.integration_deterministic
+def test_model_runs_sweep():
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
+    param_file = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
+    )
+
+    subprocess.check_call([f, f"-p {param_file}", "-w model.seed.run:1:3"])
+    assert True
+
+
 @pytest.mark.integration_deterministic
 def test_model_reproducible(tmpdir):
     path_a = tmpdir.mkdir("result_a")
     path_b = tmpdir.mkdir("result_b")
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic_seeded.yml"
     )
@@ -80,7 +97,9 @@ def test_model_reproducible(tmpdir):
 @pytest.mark.integration_deterministic
 def test_model_pop_write_read(tmpdir):
     path_a = tmpdir.mkdir("a")
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
     )
@@ -99,13 +118,17 @@ def test_model_pop_write_read(tmpdir):
 
 @pytest.mark.integration_deterministic
 def test_model_settings_run(tmpdir):
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "integration_base.yml"
     )
 
     for item in os.listdir(
-        os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "settings")
+        os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "..", "titan", "settings"
+        )
     ):
         if "__" not in item and item != "base":
             path = tmpdir.mkdir(item)