Merge branch 'env_package_list' into 'master'

Add env_package_list function to capture full environment listing

See merge request !1166

bilby/core/sampler/__init__.py

@@ -6,7 +6,7 @@ import bilby
 from bilby.bilby_mcmc import Bilby_MCMC
 
 from ..prior import DeltaFunction, PriorDict
-from ..utils import command_line_args, loaded_modules_dict, logger
+from ..utils import command_line_args, env_package_list, loaded_modules_dict, logger
 from . import proposal
 from .base_sampler import Sampler, SamplingMarginalisedParameterError
 from .cpnest import Cpnest
@@ -175,6 +175,7 @@ def run_sampler(
     likelihood.outdir = outdir
     meta_data["likelihood"] = likelihood.meta_data
     meta_data["loaded_modules"] = loaded_modules_dict()
+    meta_data["environment_packages"] = env_package_list(as_dataframe=True)
 
     if command_line_args.bilby_zero_likelihood_mode:
         from bilby.core.likelihood import ZeroLikelihood

bilby/core/utils/log.py

+import json
 import logging
 from pathlib import Path
+import subprocess
 import sys
 
 logger = logging.getLogger('bilby')
@@ -70,3 +72,60 @@ def loaded_modules_dict():
         if "." not in str(key):
             vdict[key] = str(getattr(sys.modules[key], "__version__", "N/A"))
     return vdict
+
+
+def env_package_list(as_dataframe=False):
+    """Get the list of packages installed in the system prefix.
+
+    If it is detected that the system prefix is part of a Conda environment,
+    a call to ``conda list --prefix {sys.prefix}`` will be made, otherwise
+    the call will be to ``{sys.executable} -m pip list installed``.
+
+    Parameters
+    ----------
+    as_dataframe: bool
+        return output as a `pandas.DataFrame`
+
+    Returns
+    -------
+    pkgs : `list` of `dict`, or `pandas.DataFrame`
+        If ``as_dataframe=False`` is given, the output is a `list` of `dict`,
+        one for each package, at least with ``'name'`` and ``'version'`` keys
+        (more if `conda` is used).
+        If ``as_dataframe=True`` is given, the output is a `DataFrame`
+        created from the `list` of `dicts`.
+    """
+    prefix = sys.prefix
+
+    # if a conda-meta directory exists, this is a conda environment, so
+    # use conda to print the package list
+    if (Path(prefix) / "conda-meta").is_dir():
+        pkgs = json.loads(subprocess.check_output([
+            "conda",
+            "list",
+            "--prefix", prefix,
+            "--json"
+        ]))
+
+    # otherwise try and use Pip
+    else:
+        try:
+            import pip  # noqa: F401
+        except ModuleNotFoundError:  # no pip?
+            # not a conda environment, and no pip, so just return
+            # the list of loaded modules
+            modules = loaded_modules_dict()
+            pkgs = [{"name": x, "version": y} for x, y in modules.items()]
+        else:
+            pkgs = json.loads(subprocess.check_output([
+                sys.executable,
+                "-m", "pip",
+                "list", "installed",
+                "--format", "json",
+            ]))
+
+    # convert to recarray for storage
+    if as_dataframe:
+        from pandas import DataFrame
+        return DataFrame(pkgs)
+    return pkgs