Update test suite to test warm starts

.github/workflows/CI.yml

@@ -71,8 +71,7 @@ jobs:
         run: pip install coverage coveralls
       - name: "Run tests"
         run: |
-            coverage run --source=pysr --omit='*/test/*' -m pysr test main
-            coverage run --append --source=pysr --omit='*/test/*' -m pysr test cli
+            coverage run --source=pysr --omit='*/test/*' -m pysr test main,cli,warm-start
       - name: "Install JAX"
         run: pip install jax jaxlib # (optional import)
         if: ${{ matrix.test-id == 'main' }}

.github/workflows/CI_Windows.yml

@@ -56,8 +56,7 @@ jobs:
             python -c 'import pysr'
       - name: "Run tests"
         run: |
-            python -m pysr test main
-            python -m pysr test cli
+            python -m pysr test main,cli,warm-start
       - name: "Install Torch"
         run: pip install torch # (optional import)
       - name: "Run Torch tests"

.github/workflows/CI_conda_forge.yml

@@ -40,4 +40,4 @@ jobs:
         run: conda activate pysr-test && conda install pysr
         if: ${{ !matrix.use-mamba }}
       - name: "Run tests"
-        run: python -m pysr test main
+        run: python -m pysr test main,warm-start

.github/workflows/CI_docker.yml

@@ -37,4 +37,4 @@ jobs:
       - name: Build docker
         run: docker build --platform=${{ matrix.arch }} -t pysr .
       - name: Test docker
-        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr test main && python3 -m pysr test cli'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr test main,cli,warm-start'

.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 }} --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 cli'
+        run: docker run --platform=${{ matrix.arch }} --rm pysr /bin/bash -c 'python3 -m pysr test main,cli,warm-start'

.github/workflows/CI_large_nightly.yml

@@ -47,5 +47,4 @@ jobs:
         run: python3 -c "from pysr import jl; assert jl.VERSION.major == jl.seval('v\"${{ matrix.julia-version }}\"').major; assert jl.VERSION.minor == jl.seval('v\"${{ matrix.julia-version }}\"').minor"
       - name: "Run tests"
         run: |
-            python -m pysr test main
-            python -m pysr test cli
+            python -m pysr test main,cli,warm-start

.github/workflows/CI_mac.yml

@@ -56,8 +56,7 @@ jobs:
             python -c 'import pysr'
       - name: "Run tests"
         run: |
-            python -m pysr test main
-            python -m pysr test cli
+            python -m pysr test main,cli,warm-start
       - name: "Install JAX"
         run: pip install jax jaxlib # (optional import)
       - name: "Run JAX tests"

pysr/_cli/main.py

@@ -17,15 +17,13 @@ def pysr(context):
     ctx = context
 
 
-@pysr.command("install", help="Install Julia dependencies for PySR.")
+@pysr.command("install", help="DEPRECATED (dependencies are now installed at import).")
 @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(
@@ -33,14 +31,12 @@ def pysr(context):
     "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):
     warnings.warn(
@@ -51,33 +47,25 @@ def _install(julia_project, quiet, precompile):
 TEST_OPTIONS = {"main", "jax", "torch", "cli", "warm_start"}
 
 
-@pysr.command("test", help="Run PySR test suite.")
-@click.argument("tests", nargs=-1)
+@pysr.command("test")
+@click.argument("tests", nargs=1)
 def _tests(tests):
-    """Run part of the PySR test suite.
+    """Run parts of the PySR test suite.
 
-    Choose from main, jax, torch, cli, and warm_start.
+    Choose from main, jax, torch, cli, and warm_start. You can give multiple tests, separated by commas.
     """
-    if len(tests) == 0:
-        raise click.UsageError(
-            "At least one test must be specified. "
-            + "The following are available: "
-            + ", ".join(TEST_OPTIONS)
-            + "."
-        )
-    else:
-        for test in tests:
-            if test in TEST_OPTIONS:
-                if test == "main":
-                    runtests()
-                elif test == "jax":
-                    runtests_jax()
-                elif test == "torch":
-                    runtests_torch()
-                elif test == "cli":
-                    runtests_cli = get_runtests_cli()
-                    runtests_cli()
-                elif test == "warm_start":
-                    runtests_warm_start()
-            else:
-                warnings.warn(f"Invalid test {test}. Skipping.")
+    for test in tests.split(","):
+        if test in TEST_OPTIONS:
+            if test == "main":
+                runtests()
+            elif test == "jax":
+                runtests_jax()
+            elif test == "torch":
+                runtests_torch()
+            elif test == "cli":
+                runtests_cli = get_runtests_cli()
+                runtests_cli()
+            elif test == "warm-start":
+                runtests_warm_start()
+        else:
+            warnings.warn(f"Invalid test {test}. Skipping.")

pysr/test/test_cli.py

@@ -1,4 +1,5 @@
 import unittest
+from textwrap import dedent
 
 from click import testing as click_testing
 
@@ -14,43 +15,58 @@ def get_runtests():
             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.",
-                    "",
-                ]
+            expected = dedent(
+                """
+                    Usage: pysr [OPTIONS] COMMAND [ARGS]...
+
+                    Options:
+                    --help  Show this message and exit.
+
+                    Commands:
+                    install  DEPRECATED (dependencies are now installed at import).
+                    test     Run PySR test suite.
+                """
             )
             result = self.cli_runner.invoke(pysr, ["--help"])
-            self.assertEqual(expected, result.output)
-            self.assertEqual(0, result.exit_code)
+            self.assertEqual(result.output, expected)
+            self.assertEqual(result.exit_code, 0)
 
         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.",
-                    "",
-                ]
+            expected = dedent(
+                """
+                Usage: pysr install [OPTIONS]
+
+                DEPRECATED (dependencies are now installed at import).
+
+                Options:
+                -p, --project TEXT
+                -q, --quiet         Disable logging.
+                --precompile
+                --no-precompile
+                --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)
+            self.assertEqual(result.output, expected)
+            self.assertEqual(result.exit_code, 0)
+
+        def test_help_on_test(self):
+            expected = dedent(
+                """
+                Usage: pysr test [OPTIONS] TESTS
+
+                Run parts of the PySR test suite.
+
+                Choose from main, jax, torch, cli, and warm_start. You can give multiple
+                tests, separated by commas.
+
+                Options:
+                --help  Show this message and exit.
+                """
+            )
+            result = self.cli_runner.invoke(pysr, ["test", "--help"])
+            self.assertEqual(result.output, expected)
+            self.assertEqual(result.exit_code, 0)
 
     def runtests():
         """Run all tests in cliTest.py."""