learningmachine 2.7.0__tar.gz → 2.10.0__tar.gz

{learningmachine-2.7.0 → learningmachine-2.10.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: learningmachine
-Version: 2.7.0
+Version: 2.10.0
 Summary: Machine Learning with uncertainty quantification and interpretability
 Home-page: https://github.com/Techtonique/learningmachine_python
 Author: T. Moudiki
@@ -22,5 +22,16 @@ Requires-Dist: pandas
 Requires-Dist: rpy2>=3.4.5
 Requires-Dist: scikit-learn
 Requires-Dist: scipy
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 Machine Learning with uncertainty quantification and interpretability.

{learningmachine-2.7.0 → learningmachine-2.10.0}/learningmachine.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: learningmachine
-Version: 2.7.0
+Version: 2.10.0
 Summary: Machine Learning with uncertainty quantification and interpretability
 Home-page: https://github.com/Techtonique/learningmachine_python
 Author: T. Moudiki
@@ -22,5 +22,16 @@ Requires-Dist: pandas
 Requires-Dist: rpy2>=3.4.5
 Requires-Dist: scikit-learn
 Requires-Dist: scipy
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 Machine Learning with uncertainty quantification and interpretability.

learningmachine-2.10.0/setup.py

@@ -0,0 +1,223 @@
+import os
+import platform
+import subprocess
+import sys
+
+
+def _running_noninteractively():
+    """True when there is no human at a terminal to answer a prompt.
+
+    This covers CI systems (GitHub Actions sets CI=true), any environment
+    where CI/PIP_NO_INPUT is set, and plain non-tty stdin.
+    """
+    if os.environ.get("CI") or os.environ.get("PIP_NO_INPUT"):
+        return True
+    try:
+        return not sys.stdin.isatty()
+    except Exception:
+        return True
+
+
+def _is_packaging_only_invocation():
+    """True when setup.py is only being asked to build metadata/artifacts
+    (sdist, bdist_wheel, egg_info, ...), not to actually install the
+    package. These commands run on build machines (e.g. CI building a
+    release) that don't need R/rpy2 present at all -- R is a *runtime*
+    dependency of the installed package, not a build-time one.
+    """
+    packaging_commands = {
+        "sdist", "bdist_wheel", "bdist", "egg_info", "dist_info",
+        "check", "--version", "--help", "--help-commands",
+    }
+    return any(arg in packaging_commands for arg in sys.argv[1:])
+
+
+def check_r_installed():
+    current_platform = platform.system()
+
+    if current_platform == "Windows":
+        try:
+            subprocess.run(
+                ["reg", "query", "HKLM\\Software\\R-core\\R"], check=True
+            )
+            print("R is already installed on Windows.")
+            return True
+        except (subprocess.CalledProcessError, FileNotFoundError):
+            print("R is not installed on Windows.")
+            return False
+
+    elif current_platform in ("Linux", "Darwin"):
+        try:
+            subprocess.run(["which", "R"], check=True)
+            print(f"R is already installed on {current_platform}.")
+            return True
+        except (subprocess.CalledProcessError, FileNotFoundError):
+            print(f"R is not installed on {current_platform}.")
+            return False
+
+    else:
+        print("Unsupported platform. Unable to check for R installation.")
+        return False
+
+
+def install_r():
+    current_platform = platform.system()
+
+    if current_platform == "Windows":
+        install_command = (
+            "Start-Process powershell -Verb runAs -ArgumentList "
+            "'-Command \"& {Invoke-WebRequest "
+            "https://cran.r-project.org/bin/windows/base/R-4.1.2-win.exe "
+            "-OutFile R.exe}; Start-Process R.exe -ArgumentList "
+            "'/SILENT' -Wait}'"
+        )
+        subprocess.run(install_command, shell=True)
+
+    elif current_platform == "Linux":
+        install_command = (
+            "sudo apt update -qq && "
+            "sudo apt-key adv --keyserver keyserver.ubuntu.com "
+            "--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && "
+            "sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' && "
+            "sudo apt update && "
+            "sudo apt -y install r-base"
+        )
+        subprocess.run(install_command, shell=True)
+
+    elif current_platform == "Darwin":
+        subprocess.run("brew install r", shell=True)
+
+    else:
+        print("Unsupported platform. Unable to install R.")
+
+
+def install_packages():
+    """Install the R-side dependencies, retrying into a local library
+    ('r-learningmachine') if the default library isn't writable."""
+    attempts = [
+        {"lib": None},
+        {"lib": "r-learningmachine"},
+    ]
+
+    for attempt in attempts:
+        lib = attempt["lib"]
+        lib_arg = f", lib='{lib}'" if lib else ""
+        try:
+            if lib:
+                subprocess.run(["mkdir", "-p", lib], check=True)
+            subprocess.run(
+                ["Rscript", "-e",
+                 f"utils::install.packages('remotes', dependencies=TRUE{lib_arg})"],
+                check=True,
+            )
+            subprocess.run(
+                ["Rscript", "-e",
+                 f"utils::install.packages(c('R6', 'Rcpp', 'skimr'), dependencies=TRUE{lib_arg})"],
+                check=True,
+            )
+            subprocess.run(
+                ["Rscript", "-e",
+                 f"remotes::install_github('Techtonique/learningmachine'{lib_arg})"],
+                check=True,
+            )
+            print(f"R package installation succeeded (lib={lib!r}).")
+            return True
+        except subprocess.CalledProcessError as e:
+            print(f"Error occurred while installing R packages (lib={lib!r}): {e}")
+            print(f"Return code: {e.returncode}")
+
+    print(
+        "Warning: could not install the R 'learningmachine' package "
+        "automatically. Install it manually, e.g.:\n"
+        "  Rscript -e \"remotes::install_github('Techtonique/learningmachine')\""
+    )
+    return False
+
+
+def ensure_r_available():
+    """Make sure R is present, installing it (or asking to) only when it
+    actually makes sense to do so."""
+    if check_r_installed():
+        print("No R installation needed.")
+        return
+
+    if _running_noninteractively():
+        if os.environ.get("LEARNINGMACHINE_AUTO_INSTALL_R") == "1":
+            print("Non-interactive environment: auto-installing R "
+                  "(LEARNINGMACHINE_AUTO_INSTALL_R=1 was set).")
+            install_r()
+        else:
+            print(
+                "R is not installed and this looks like a non-interactive "
+                "environment (CI or no TTY), so setup.py will NOT prompt "
+                "for input and will NOT attempt to install R automatically.\n"
+                "Set the environment variable LEARNINGMACHINE_AUTO_INSTALL_R=1 "
+                "before running setup.py if you want it to try installing R, "
+                "or install R yourself first: https://cloud.r-project.org/"
+            )
+        return
+
+    # Interactive session with a real human at a terminal.
+    try:
+        install_r_prompt = int(input("Try installing R? 1-yes, 2-no: "))
+    except (EOFError, ValueError):
+        install_r_prompt = 2
+
+    if install_r_prompt == 1:
+        print("Installing R...")
+        install_r()
+    else:
+        print(
+            "Skipping R installation. Install R manually first: "
+            "https://cloud.r-project.org/"
+        )
+
+
+# Building an sdist/wheel (e.g. in CI to publish a release) never needs R
+# or rpy2 on the build machine -- those are runtime dependencies for
+# whoever installs the package. Only run the R setup dance for actual
+# install-type invocations.
+if not _is_packaging_only_invocation():
+    ensure_r_available()
+    if check_r_installed():
+        install_packages()
+    subprocess.run([sys.executable, "-m", "pip", "install", "rpy2"])
+else:
+    print(f"Packaging-only invocation ({' '.join(sys.argv[1:])}); "
+          "skipping R/rpy2 setup.")
+
+from setuptools import setup, find_packages
+from codecs import open
+from os import path
+
+# 4 - Package setup -----------------------------------------------
+
+"""The setup script."""
+
+setup(
+    author="T. Moudiki",
+    author_email="thierry.moudiki@gmail.com",
+    python_requires=">=3.6",
+    classifiers=[
+        "Development Status :: 2 - Pre-Alpha",
+        "Intended Audience :: Developers",
+        "License :: OSI Approved :: BSD License",
+        "Natural Language :: English",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+    ],
+    description="Machine Learning with uncertainty quantification and interpretability",
+    install_requires=['numpy', 'pandas', 'rpy2>=3.4.5', 'scikit-learn', 'scipy'],
+    license="BSD Clause Clear license",
+    long_description="Machine Learning with uncertainty quantification and interpretability.",
+    include_package_data=True,
+    keywords="learningmachine",
+    name="learningmachine",
+    packages=find_packages(include=["learningmachine", "learningmachine.*"]),
+    test_suite="tests",
+    url="https://github.com/Techtonique/learningmachine_python",
+    version="2.10.0",
+    zip_safe=False,
+)

learningmachine-2.7.0/setup.py

@@ -1,174 +0,0 @@
-import platform
-import subprocess
-
-def check_r_installed():
-    current_platform = platform.system()
-
-    if current_platform == "Windows":
-        # Check if R is installed on Windows by checking the registry
-        try:
-            subprocess.run(
-                ["reg", "query", "HKLM\\Software\\R-core\\R"], check=True
-            )
-            print("R is already installed on Windows.")
-            return True
-        except subprocess.CalledProcessError:
-            print("R is not installed on Windows.")
-            return False
-
-    elif current_platform == "Linux":
-        # Check if R is installed on Linux by checking if the 'R' executable is available
-        try:
-            subprocess.run(["which", "R"], check=True)
-            print("R is already installed on Linux.")
-            return True
-        except subprocess.CalledProcessError:
-            print("R is not installed on Linux.")
-            return False
-
-    elif current_platform == "Darwin":  # macOS
-        # Check if R is installed on macOS by checking if the 'R' executable is available
-        try:
-            subprocess.run(["which", "R"], check=True)
-            print("R is already installed on macOS.")
-            return True
-        except subprocess.CalledProcessError:
-            print("R is not installed on macOS.")
-            return False
-
-    else:
-        print("Unsupported platform. Unable to check for R installation.")
-        return False
-
-def install_r():
-
-    current_platform = platform.system()
-
-    if current_platform == "Windows":
-        # Install R on Windows using PowerShell
-        install_command = "Start-Process powershell -Verb subprocess.runAs -ArgumentList '-Command \"& {Invoke-WebRequest https://cran.r-project.org/bin/windows/base/R-4.1.2-win.exe -OutFile R.exe}; Start-Process R.exe -ArgumentList '/SILENT' -Wait}'"
-        subprocess.run(install_command, shell=True)
-
-    elif current_platform == "Linux":
-        # Install R on Linux using the appropriate package manager (e.g., apt-get)
-        install_command = (
-            "sudo apt update -qq && sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9"
-            + "&& sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'"
-            + "&& sudo apt update"
-            + "&& sudo apt -y install r-base"
-        )
-        subprocess.run(install_command, shell=True)
-
-    elif current_platform == "Darwin":  # macOS
-        # Install R on macOS using Homebrew
-        install_command = "brew install r"
-        subprocess.run(install_command, shell=True)
-
-    else:
-
-        print("Unsupported platform. Unable to install R.")
-
-def install_packages():
-    try: 
-        subprocess.run(["Rscript", "-e", "utils::install.packages('remotes', dependencies=TRUE)"])
-        subprocess.run(["Rscript", "-e", "utils::install.packages(c('R6', 'Rcpp', 'skimr'), dependencies=TRUE)"])
-        subprocess.run(["Rscript", "-e", "remotes::install_github('Techtonique/learningmachine')"])        
-    except subprocess.CalledProcessError as e:
-        print(f"Error occurred: {e}")
-        print(f"Return code: {e.returncode}")
-        print(f"Output: {e.output}")
-        print(f"Stderr: {e.stderr}")
-        try:
-            subprocess.run(["mkdir", "-p", "r-learningmachine"])		 
-            subprocess.run(["Rscript", "-e", "utils::install.packages('remotes', lib='r-learningmachine', dependencies=TRUE)"])
-            subprocess.run(["Rscript", "-e", "utils::install.packages(c('R6', 'Rcpp', 'skimr'), lib='r-learningmachine', dependencies=TRUE)"])
-            subprocess.run(["Rscript", "-e", "remotes::install_github('Techtonique/learningmachine', lib='r-learningmachine')"])
-        except subprocess.CalledProcessError as e:    
-            print(f"Error occurred: {e}")
-            print(f"Return code: {e.returncode}")
-            print(f"Output: {e.output}")
-            print(f"Stderr: {e.stderr}")        
-            try:	
-                subprocess.run(["Rscript", "-e", "utils::install.packages('remotes', dependencies=TRUE)"])
-                subprocess.run(["Rscript", "-e", "utils::install.packages(c('R6', 'Rcpp', 'skimr'), dependencies=TRUE)"])
-                subprocess.run(["Rscript", "-e", "remotes::install_github('Techtonique/learningmachine')"])        
-            except subprocess.CalledProcessError as e:	
-                print(f"Error occurred: {e}")
-                print(f"Return code: {e.returncode}")
-                print(f"Output: {e.output}")
-                print(f"Stderr: {e.stderr}")        
-                try: 
-                    subprocess.run(["mkdir", "-p", "r-learningmachine"])		 
-                    subprocess.run(["Rscript", "-e", "utils::install.packages('remotes', lib='r-learningmachine', dependencies=TRUE)"])
-                    subprocess.run(["Rscript", "-e", "utils::install.packages(c('R6', 'Rcpp', 'skimr'), lib='r-learningmachine', dependencies=TRUE)"])
-                    subprocess.run(["Rscript", "-e", "remotes::install_github('Techtonique/learningmachine', lib='r-learningmachine')"])
-                except subprocess.CalledProcessError as e:
-                    print(f"Error occurred: {e}")
-                    print(f"Return code: {e.returncode}")
-                    print(f"Output: {e.output}")
-                    print(f"Stderr: {e.stderr}")        
-                    try:	
-                        subprocess.run(["Rscript", "-e", "utils::install.packages('remotes', dependencies=TRUE)"])
-                        subprocess.run(["Rscript", "-e", "utils::install.packages(c('R6', 'Rcpp', 'skimr'), dependencies=TRUE)"])
-                        subprocess.run(["Rscript", "-e", "remotes::install_github('Techtonique/learningmachine')"])
-                    except subprocess.CalledProcessError as e:	
-                        print(f"Error occurred: {e}")
-                        print(f"Return code: {e.returncode}")
-                        print(f"Output: {e.output}")
-                        print(f"Stderr: {e.stderr}")        
-                        subprocess.run(["mkdir", "-p", "r-learningmachine"])		 
-                        subprocess.run(["Rscript", "-e", "utils::install.packages('remotes', lib='r-learningmachine', dependencies=TRUE)"])
-                        subprocess.run(["Rscript", "-e", "utils::install.packages(c('R6', 'Rcpp', 'skimr'), lib='r-learningmachine', dependencies=TRUE)"])
-                        subprocess.run(["Rscript", "-e", "remotes::install_github('Techtonique/learningmachine', lib='r-learningmachine')"])
-
-
-# Check if R is installed; if not, install it
-if not check_r_installed():
-    install_r_prompt = int(input("Try installing R? 1-yes, 2-no"))
-    if install_r_prompt == 1: 
-        print("Installing R...")
-        install_r()
-    else:
-        raise ValueError('Try installing R manually first.')
-else:
-    print("No R installation needed.")
-
-install_packages()
-
-subprocess.run(["pip", "install", "rpy2"])
-
-from setuptools import setup, find_packages
-from codecs import open
-from os import path
-
-# 4 - Package setup -----------------------------------------------
-    
-"""The setup script."""
-
-setup(
-    author="T. Moudiki",
-    author_email="thierry.moudiki@gmail.com",
-    python_requires=">=3.6",
-    classifiers=[
-        "Development Status :: 2 - Pre-Alpha",
-        "Intended Audience :: Developers",
-        "License :: OSI Approved :: BSD License",
-        "Natural Language :: English",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-    ],
-    description="Machine Learning with uncertainty quantification and interpretability",
-    install_requires=['numpy', 'pandas', 'rpy2>=3.4.5', 'scikit-learn', 'scipy'],
-    license="BSD Clause Clear license",
-    long_description="Machine Learning with uncertainty quantification and interpretability.",
-    include_package_data=True,
-    keywords="learningmachine",
-    name="learningmachine",
-    packages=find_packages(include=["learningmachine", "learningmachine.*"]),
-    test_suite="tests",
-    url="https://github.com/Techtonique/learningmachine_python",
-    version="2.7.0",
-    zip_safe=False,
-)