Merge branch 'master' into joss

.github/workflows/python.yaml

@@ -5,10 +5,11 @@ on: [push, pull_request]
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest]
 
     steps:
       - uses: actions/checkout@v3

README.rst

@@ -2,28 +2,46 @@
 otoole: OSeMOSYS tools for energy work
 ==================================================
 
-.. image:: https://coveralls.io/repos/github/OSeMOSYS/otoole/badge.svg?branch=master&kill_cache=1
-    :target: https://coveralls.io/github/OSeMOSYS/otoole?branch=master
+.. image:: https://joss.theoj.org/papers/e93a191ae795b171beff782a68fdc467/status.svg
+    :target: https://joss.theoj.org/papers/e93a191ae795b171beff782a68fdc467
+    :alt: JOSS status
 
-.. image:: https://readthedocs.org/projects/otoole/badge/?version=latest
-    :target: https://otoole.readthedocs.io/en/latest/?badge=latest
-    :alt: Documentation Status
+.. image:: https://img.shields.io/pypi/v/otoole.svg
+    :target: https://pypi.org/project/otoole/
+    :alt: PyPI
 
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/psf/black
+    :alt: Code Style
 
-.. image:: https://joss.theoj.org/papers/e93a191ae795b171beff782a68fdc467/status.svg
-    :target: https://joss.theoj.org/papers/e93a191ae795b171beff782a68fdc467
-    :alt: JOSS status
+.. image:: https://img.shields.io/badge/python-3.9_|_3.10_|_3.11-blue.svg
+    :target: https://crate.io/packages/otoole/
+    :alt: Python Version
 
-A Python toolkit to support use of OSeMOSYS
+.. image:: https://img.shields.io/badge/License-MIT-green.svg
+    :target: https://opensource.org/licenses/MIT
+    :alt: License
+
+|
+
+.. image:: https://coveralls.io/repos/github/OSeMOSYS/otoole/badge.svg?branch=master&kill_cache=1
+    :target: https://coveralls.io/github/OSeMOSYS/otoole?branch=master
+    :alt: Code Coverage
+
+.. image:: https://github.com/OSeMOSYS/otoole/actions/workflows/python.yaml/badge.svg?branch=master
+    :target: https://github.com/OSeMOSYS/otoole/actions/workflows/python.yaml
+    :alt: GitHub CI
+
+.. image:: https://readthedocs.org/projects/otoole/badge/?version=latest
+    :target: https://otoole.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
 
 Description
 ===========
 
 OSeMOSYS tools for energy work, or otoole, is a Python package
-which provides a command-line interface for users of OSeMOSYS. The aim of the
-package is to provide commonly used pre- and post-processing steps for OSeMOSYS.
+to support the users of OSeMOSYS. The aim of the package is to provide commonly
+used pre- and post-processing steps for OSeMOSYS.
 
 **otoole** aims to support different ways of storing input data and results,
 including csv files and Excel workbooks, as well as different implementations
@@ -53,5 +71,7 @@ Contributing
 
 New ideas and bugs `should be submitted <https://github.com/OSeMOSYS/otoole/issues/new>`_
 to the repository issue tracker. Please do contribute by discussing and developing these
-ideas further. To contribute directly to the documentation of code development, please see
-the contribution guidelines document.
+ideas further.
+
+To contribute directly to the code and documentation development, please see
+the `contribution guidelines <https://otoole.readthedocs.io/en/latest/contributing.html>`_.

docs/examples.rst

@@ -215,7 +215,20 @@ Run the following command, where the RES will be saved as the file ``res.png``::
 
     $ otoole viz res excel simplicity.xlsx res.png config.yaml
 
-2. View the RES
+.. WARNING::
+    If you encounter a ``graphviz`` dependency error, install it on your system
+    from the graphviz_ website (if on Windows) or via the command::
+
+        sudo apt install graphviz # if on Ubuntu
+        brew install graphviz # if on Mac
+
+    To check that ``graphviz`` installed correctly, run ``dot -V`` to check the
+    version::
+
+        ~$ dot -V
+        dot - graphviz version 2.43.0 (0)
+
+1. View the RES
 ~~~~~~~~~~~~~~~
 Open the newly created file, ``res.png`` and the following image should be
 displayed
@@ -311,8 +324,12 @@ The MathProg datafile describing this model can be found on the
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Create a configuration validation ``yaml`` file::
 
+    # on UNIX
     $ touch validate.yaml
 
+    # on Windows
+    > type nul > validate.yaml
+
 3. Create ``FUEL`` Codes
 ~~~~~~~~~~~~~~~~~~~~~~~~
 Create the fuel codes and descriptions in the validation configuration file::
@@ -486,3 +503,4 @@ will also flag it as an isolated fuel. This means the fuel is unconnected from t
 .. _CPLEX: https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer
 .. _Anaconda: https://www.anaconda.com/
 .. _Gurobi: https://www.gurobi.com/
+.. _graphviz: https://www.graphviz.org/download/

src/otoole/input.py

@@ -116,7 +116,6 @@ def convert(self, input_filepath: str, output_filepath: str, **kwargs: Dict):
 
 class Strategy(ABC):
     """
-
     Arguments
     ---------
     user_config : dict, default=None
@@ -139,10 +138,20 @@ def _add_dtypes(self, config: Dict):
                 dtypes = {}
                 for column in details["indices"] + ["VALUE"]:
                     if column == "VALUE":
-                        dtypes["VALUE"] = details["dtype"]
+                        dtypes["VALUE"] = (
+                            details["dtype"] if details["dtype"] != "int" else "int64"
+                        )
                     else:
-                        dtypes[column] = config[column]["dtype"]
+                        dtypes[column] = (
+                            config[column]["dtype"]
+                            if config[column]["dtype"] != "int"
+                            else "int64"
+                        )
                 details["index_dtypes"] = dtypes
+            elif details["type"] == "set":
+                details["dtype"] = (
+                    details["dtype"] if details["dtype"] != "int" else "int64"
+                )
         return config
 
     @property
@@ -491,8 +500,8 @@ def _check_index_dtypes(
             except ValueError:  # ValueError: invalid literal for int() with base 10:
                 df = df.dropna(axis=0, how="all").reset_index()
                 for index, dtype in config["index_dtypes"].items():
-                    if dtype == "int":
-                        df[index] = df[index].astype(float).astype(int)
+                    if dtype == "int64":
+                        df[index] = df[index].astype(float).astype("int64")
                     else:
                         df[index] = df[index].astype(dtype)
                 df = df.set_index(config["indices"])

src/otoole/results/result_package.py

@@ -858,7 +858,7 @@ def discount_factor(
     if regions and years:
         discount_rate["YEAR"] = [years]
         discount_factor = discount_rate.explode("YEAR").reset_index(level="REGION")
-        discount_factor["YEAR"] = discount_factor["YEAR"].astype(int)
+        discount_factor["YEAR"] = discount_factor["YEAR"].astype("int64")
         discount_factor["NUM"] = discount_factor["YEAR"] - discount_factor["YEAR"].min()
         discount_factor["RATE"] = discount_factor["VALUE"] + 1
         discount_factor["VALUE"] = (

src/otoole/results/results.py

@@ -347,7 +347,7 @@ def read_model(self, file_path: Union[str, TextIO]) -> pd.DataFrame:
         df["INDEX"] = df["INDEX"].map(lambda x: x.split("]")[0])
         df = (
             df[["ID", "NUM", "NAME", "INDEX"]]
-            .astype({"ID": str, "NUM": int, "NAME": str, "INDEX": str})
+            .astype({"ID": str, "NUM": "int64", "NAME": str, "INDEX": str})
             .reset_index(drop=True)
         )
 
@@ -425,7 +425,7 @@ def read_solution(
         data = (
             data[["ID", "NUM", "STATUS", "PRIM", "DUAL"]]
             .astype(
-                {"ID": str, "NUM": int, "STATUS": str, "PRIM": float, "DUAL": float}
+                {"ID": str, "NUM": "int64", "STATUS": str, "PRIM": float, "DUAL": float}
             )
             .reset_index(drop=True)
         )

src/otoole/write_strategies.py

@@ -156,7 +156,12 @@ def _write_parameter(
             df = self._form_parameter(df, default)
         handle.write("param default {} : {} :=\n".format(default, parameter_name))
         df.to_csv(
-            path_or_buf=handle, sep=" ", header=False, index=True, float_format="%g"
+            path_or_buf=handle,
+            sep=" ",
+            header=False,
+            index=True,
+            float_format="%g",
+            lineterminator="\n",
         )
         handle.write(";\n")
 
@@ -171,7 +176,12 @@ def _write_set(self, df: pd.DataFrame, set_name, handle: TextIO):
         """
         handle.write("set {} :=\n".format(set_name))
         df.to_csv(
-            path_or_buf=handle, sep=" ", header=False, index=False, float_format="%g"
+            path_or_buf=handle,
+            sep=" ",
+            header=False,
+            index=False,
+            float_format="%g",
+            lineterminator="\n",
         )
         handle.write(";\n")