Merge pull request #298 from w2ll2am/master

Added CLI to run pysr.install() to install Julia dependencies

.github/workflows/CI.yml

@@ -54,11 +54,13 @@ jobs:
             python -m pip install --upgrade pip
             pip install -r requirements.txt
             python setup.py install
-            python -c 'import pysr; pysr.install()'
+            python -m pysr install
       - name: "Install Coverage tool"
         run: pip install coverage coveralls
       - name: "Run tests"
-        run: coverage run --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test main
+        run: |
+            coverage run --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test main
+            coverage run --append --source=pysr --omit='*/test/*,*/feynman_problems.py' -m pysr.test cli
       - name: "Install JAX"
         run: pip install jax jaxlib # (optional import)
       - name: "Run JAX tests"
@@ -112,7 +114,7 @@ jobs:
       - name: "Install PySR"
         run: |
             python3 -m pip install .
-            python3 -c 'import pysr; pysr.install()'
+            python3 -m pysr install
       - name: "Run tests"
         run: cd /tmp && python -m pysr.test main
 

.github/workflows/CI_Windows.yml

@@ -54,9 +54,11 @@ jobs:
             python -m pip install --upgrade pip
             pip install -r requirements.txt
             python setup.py install
-            python -c 'import pysr; pysr.install()'
+            python -m pysr install
       - name: "Run tests"
-        run: python -m pysr.test main
+        run: |
+            python -m pysr.test main
+            python -m pysr.test cli
       - name: "Install Torch"
         run: pip install torch # (optional import)
       - name: "Run Torch tests"

.github/workflows/CI_docker.yml

@@ -39,4 +39,4 @@ jobs:
       - name: Build docker
         run: docker build --platform=${{ matrix.arch }} -t pysr --build-arg JLVERSION=${{ matrix.julia-version }} --build-arg PYVERSION=${{ matrix.python-version }} .
       - name: Test docker
-        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test env'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test cli && python3 -m pysr.test env'

.github/workflows/CI_docker_large_nightly.yml

@@ -33,4 +33,4 @@ jobs:
       - name: Build docker
         run: docker build --platform=${{ matrix.arch }} -t pysr --build-arg JLVERSION=${{ matrix.julia-version }} .
       - name: Test docker
-        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test env'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr.test main && python3 -m pysr.test cli && python3 -m pysr.test env'

.github/workflows/CI_large_nightly.yml

@@ -42,9 +42,11 @@ jobs:
             python -m pip install --upgrade pip
             pip install -r requirements.txt
             python setup.py install
-            python -c 'import pysr; pysr.install()'
+            python -m pysr install
       - name: "Run tests"
-        run: python -m pysr.test main
+        run: |
+            python -m pysr.test main
+            python -m pysr.test cli
       - name: "Run new env test"
         run: python -m pysr.test env
         if: ${{ !(matrix.os == 'windows-latest' && matrix.python-version == '3.7') }}

.github/workflows/CI_mac.yml

@@ -54,9 +54,11 @@ jobs:
             python -m pip install --upgrade pip
             pip install -r requirements.txt
             python setup.py install
-            python -c 'import pysr; pysr.install()'
+            python -m pysr install
       - name: "Run tests"
-        run: python -m pysr.test main
+        run: |
+            python -m pysr.test main
+            python -m pysr.test cli
       - name: "Install JAX"
         run: pip install jax jaxlib # (optional import)
       - name: "Run JAX tests"

Dockerfile

@@ -28,7 +28,7 @@ ADD ./pysr/ /pysr/pysr/
 RUN pip3 install .
 
 # Install Julia pre-requisites:
-RUN python3 -c 'import pysr; pysr.install()'
+RUN python3 -m pysr install
 
 # metainformation
 LABEL org.opencontainers.image.authors = "Miles Cranmer"

environment.yml

@@ -9,4 +9,5 @@ dependencies:
   - setuptools
   - pyjulia
   - openlibm
-  - openspecfun
+  - openspecfun
+  - click

pysr/__main__.py

@@ -0,0 +1,4 @@
+from pysr._cli.main import pysr as _cli
+
+if __name__ == "__main__":
+    _cli(prog_name="pysr")

pysr/_cli/main.py

@@ -0,0 +1,37 @@
+import click
+from ..julia_helpers import install
+
+
+@click.group("pysr")
+@click.pass_context
+def pysr(context):
+    ctx = context
+
+
+@pysr.command("install", help="Install Julia dependencies for PySR.")
+@click.option(
+    "-p",
+    "julia_project",
+    "--project",
+    default=None,
+    type=str,
+    help="Install in a specific Julia project (e.g., a local copy of SymbolicRegression.jl).",
+    metavar="PROJECT_DIRECTORY",
+)
+@click.option("-q", "--quiet", is_flag=True, default=False, help="Disable logging.")
+@click.option(
+    "--precompile",
+    "precompile",
+    flag_value=True,
+    default=None,
+    help="Force precompilation of Julia libraries.",
+)
+@click.option(
+    "--no-precompile",
+    "precompile",
+    flag_value=False,
+    default=None,
+    help="Disable precompilation.",
+)
+def _install(julia_project, quiet, precompile):
+    install(julia_project, quiet, precompile)

pysr/export_latex.py

@@ -96,7 +96,6 @@ def generate_single_table(
                         "$" + output_variable_name + " = " + latex_equation + "$"
                     )
                 else:
-
                     broken_latex_equation = " ".join(
                         [
                             r"\begin{minipage}{0.8\linewidth}",

pysr/julia_helpers.py

@@ -110,10 +110,8 @@ def install(julia_project=None, quiet=False, precompile=None):  # pragma: no cov
 
 def _import_error():
     return """
-    Required dependencies are not installed or built.  Run the following code in the Python REPL:
-
-        >>> import pysr
-        >>> pysr.install()
+    Required dependencies are not installed or built.  Run the following command in your terminal:
+        python3 -m pysr install
     """
 
 
@@ -286,14 +284,14 @@ def _backend_version_assertion(Main):
                 f"does not match expected version {expected_backend_version}. "
                 "Things may break. "
                 "Please update your PySR installation with "
-                "`python -c 'import pysr; pysr.install()'`."
+                "`python3 -m pysr install`."
             )
     except JuliaError:  # pragma: no cover
         warnings.warn(
             "You seem to have an outdated version of SymbolicRegression.jl. "
             "Things may break. "
             "Please update your PySR installation with "
-            "`python -c 'import pysr; pysr.install()'`."
+            "`python3 -m pysr install`."
         )
 
 

pysr/test/__init__.py

@@ -2,3 +2,4 @@
 from .test_env import runtests as runtests_env
 from .test_jax import runtests as runtests_jax
 from .test_torch import runtests as runtests_torch
+from .test_cli import runtests as runtests_cli

pysr/test/__main__.py

@@ -11,7 +11,7 @@
     parser.add_argument(
         "test",
         nargs="*",
-        help="Test to run. One or more of 'main', 'env', 'jax', 'torch'.",
+        help="Test to run. One or more of 'main', 'env', 'jax', 'torch', 'cli'.",
     )
 
     # Parse args:
@@ -25,7 +25,7 @@
 
     # Run tests:
     for test in tests:
-        if test in {"main", "env", "jax", "torch"}:
+        if test in {"main", "env", "jax", "torch", "cli"}:
             cur_dir = os.path.dirname(os.path.abspath(__file__))
             print(f"Running test from {cur_dir}")
             if test == "main":
@@ -36,6 +36,8 @@
                 runtests_jax()
             elif test == "torch":
                 runtests_torch()
+            elif test == "cli":
+                runtests_cli()
         else:
             parser.print_help()
             raise SystemExit(1)

pysr/test/test_cli.py

@@ -0,0 +1,57 @@
+import unittest
+from click import testing as click_testing
+from .._cli.main import pysr
+
+
+class TestCli(unittest.TestCase):
+    # TODO: Include test for custom project here.
+    def setUp(self):
+        self.cli_runner = click_testing.CliRunner()
+
+    def test_help_on_all_commands(self):
+        expected = "\n".join(
+            [
+                "Usage: pysr [OPTIONS] COMMAND [ARGS]...",
+                "",
+                "Options:",
+                "  --help  Show this message and exit.",
+                "",
+                "Commands:",
+                "  install  Install Julia dependencies for PySR.",
+                "",
+            ]
+        )
+        result = self.cli_runner.invoke(pysr, ["--help"])
+        self.assertEqual(expected, result.output)
+        self.assertEqual(0, result.exit_code)
+
+    def test_help_on_install(self):
+        expected = "\n".join(
+            [
+                "Usage: pysr install [OPTIONS]",
+                "",
+                "  Install Julia dependencies for PySR.",
+                "",
+                "Options:",
+                "  -p, --project PROJECT_DIRECTORY",
+                "                                  Install in a specific Julia project (e.g., a",
+                "                                  local copy of SymbolicRegression.jl).",
+                "  -q, --quiet                     Disable logging.",
+                "  --precompile                    Force precompilation of Julia libraries.",
+                "  --no-precompile                 Disable precompilation.",
+                "  --help                          Show this message and exit.",
+                "",
+            ]
+        )
+        result = self.cli_runner.invoke(pysr, ["install", "--help"])
+        self.assertEqual(expected, result.output)
+        self.assertEqual(0, result.exit_code)
+
+
+def runtests():
+    """Run all tests in cliTest.py."""
+    loader = unittest.TestLoader()
+    suite = unittest.TestSuite()
+    suite.addTests(loader.loadTestsFromTestCase(TestCli))
+    runner = unittest.TextTestRunner()
+    return runner.run(suite)

pysr/version.py

@@ -1,2 +1,2 @@
-__version__ = "0.13.0"
+__version__ = "0.14.0"
 __symbolic_regression_jl_version__ = "0.18.0"

requirements.txt

@@ -1,5 +1,7 @@
 sympy
 pandas
 numpy
-scikit_learn >= 1.0.0
-julia >= 0.6.0
+scikit_learn>=1.0.0
+julia>=0.6.0
+click>=7.0.0
+setuptools>=50.0.0