Merge pull request #175 from metawards/feature_cythonise

Feature cythonise

doc/source/install.rst

@@ -4,7 +4,9 @@ Installation instructions
 
 MetaWards is a Python package, but it does come with R wrappers. This
 means that you can choose to install MetaWards either via Python or
-via R.
+via R. Note that MetaWards depends on data files that are
+held in MetaWardsData. To use MetaWards, you must install MetaWardsData
+following :doc:`these instructions <model_data>`.
 
 Installation via Python
 =======================
@@ -85,7 +87,8 @@ Once installed, you can run `metawards` by typing
 
     metawards --version
 
-This should print out some version information about MetaWards.
+This should print out some version information about MetaWards,
+including whether or not it found MetaWardsData.
 
 If this doesn't work, then it is possible that the directory into which
 `metawards` has been placed is not in your PATH (this is quite
@@ -114,7 +117,8 @@ by default in R is too old to run MetaWards (MetaWards needs
 Python 3.7 or newer, while the default in reticulate is to install
 and use Python 3.6).
 
-Once you have MetaWards installed in Python, you first need to
+Once you have MetaWards (and MetaWardsData)
+installed in Python, you first need to
 get the reticulate command that you will need to tell R which
 Python interpreter to use. We have written a function to do
 this for you. Open Python and type;

doc/source/quickstart/01_R.rst

@@ -18,6 +18,12 @@ the case by typing;
 
 If you don't see ``TRUE`` returned, then double-check your installation.
 
+.. note::
+
+   You also need to have installed MetaWardsData. If you have
+   not installed MetaWardsData then you need to install it by
+   following :doc:`these instructions <../model_data>`.
+
 Now make sure that you have installed the
 `tidyverse <https://www.tidyverse.org>`__, e.g. via;
 

doc/source/quickstart/01_console.rst

@@ -15,6 +15,12 @@ type;
 You should see that MetaWards version information is printed to the screen.
 If not, then you need to :doc:`install MetaWards <../install>`.
 
+.. note::
+
+   The output should show that MetaWardsData has been found. If you have
+   not installed MetaWardsData then you need to install it by
+   following :doc:`these instructions <../model_data>`.
+
 You also need to be able to use a text editor, e.g. notepad, vim, emacs,
 nano or pico. This quick start will use nano. Please use the editor
 that you prefer.

doc/source/quickstart/01_python.rst

@@ -28,6 +28,12 @@ analysing and plotting the results.
 
    >>> import pandas as pd
 
+.. note::
+
+   You also need to have installed MetaWardsData. If you have
+   not installed MetaWardsData then you need to install it by
+   following :doc:`these instructions <../model_data>`.
+
 Importing metawards
 -------------------
 

doc/source/quickstart/index.rst

@@ -6,7 +6,10 @@ Quick Start Guide
 
    Please make sure you have installed ``metawards``, e.g. by following these
    :doc:`installation instructions <../install>`. You can test this by
-   typing ``metawards --version`` on the terminal/console.
+   typing ``metawards --version`` on the terminal/console. Note that this
+   should show that MetaWardsData has been found. If you have
+   not installed MetaWardsData then you need to install it by
+   following :doc:`these instructions <../model_data>`.
 
 You have three choices for how you use MetaWards, and thus three choices
 for how you will follow this quick start guide;

setup.py

@@ -153,7 +153,8 @@ def get_openmp_flag():
                                              extra_postargs=[flag])
                 except Exception:
                     # We are likely missing the path to the libomp library - get this path
-                    print("\nCould not link - trying again, specifying the path to libomp")
+                    print(
+                        "\nCould not link - trying again, specifying the path to libomp")
 
                     compiler_dir = os.path.dirname(compiler.compiler_so[0])
                     libomp = glob(f"{compiler_dir}/../lib*/libomp*")
@@ -389,14 +390,35 @@ def no_cythonize(extensions, **_ignore):
         dev_requires = fp.read().strip().split("\n")
 
     if IS_WINDOWS:
-        mw_random_lib = glob("build/*/metawards.lib")
+        import sys
+        v = sys.version_info
+        print(os.getcwd())
+        print(f"build/*{v.major}.{v.minor}/metawards_random.lib")
+        mw_random_lib = glob(
+            f"build/*{v.major}.{v.minor}/metawards_random.lib")
+
+        if len(mw_random_lib) == 0:
+            if not is_build:
+                print("WARNING: CANNOT FIND metawards_random.lib!")
+        elif len(mw_random_lib) > 1:
+            mw_random_lib = [mw_random_lib[0]]
+
         libs_dir = os.path.abspath(os.path.join(sys.prefix, "libs"))
 
-        if not os.path.exists(libs_dir):
-            print(f"Cannot find libs directory? {libs_dir}")
-            raise RuntimeError(f"Cannot find libs directory {libs_dir}")
+        if not is_build:
+            print(f"Installing {mw_random_lib} to {libs_dir}")
     else:
-        mw_random_lib = glob("build/*/libmetawards_random.a")
+        import sys
+        v = sys.version_info
+        mw_random_lib = glob(
+            f"build/*{v.major}.{v.minor}/libmetawards_random.a")
+
+        if len(mw_random_lib) == 0:
+            if not is_build:
+                print("WARNING: CANNOT FIND metawards_random.lib!")
+        elif len(mw_random_lib) > 1:
+            mw_random_lib = [mw_random_lib[0]]
+
         libs_dir = "lib"
 
     setup(

src/metawards/_interpret.py

@@ -159,6 +159,19 @@ def random_number(s: str = None, rng=None, minval: float = None,
         from .utils._ran_binomial import ran_uniform
         return rmin + ((rmax - rmin) * ran_uniform(rng))
 
+    @staticmethod
+    def list(s: any):
+        """Interpret and return a list from the passed string 's'"""
+        try:
+            import ast
+            my_list = []
+            for val in ast.literal_eval(s):
+                my_list.append(val)
+
+            return my_list
+        except Exception:
+            raise ValueError(f"Cannot interpret a list from {s}")
+
     @staticmethod
     def integer(s: any, rng=None, minval: int = None,
                 maxval: int = None) -> int: