Edited create_dataset arguments to handle strings in data

.github/workflows/docs.yml

@@ -2,16 +2,14 @@ name: docs
 
 on:
   push:
-    branches: [master, main]
-  #pull_request: TODO: Enable me
-  #  branches:[master, main]
+    branches: [main]
 
 jobs:
   tests:
     name: "Build docs"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
         id: setup_python

.github/workflows/tests.yml

@@ -2,13 +2,13 @@ name: tests
 
 on:
   push:
-    branches: [master, main]
+    branches: [main]
   pull_request:
-    branches: [master, main]
+    branches: [main]
 
 jobs:
   tests:
-    name: "Run tests on py${{ matrix.python-version }}"
+    name: 'Run tests on py${{ matrix.python-version }}'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -18,9 +18,6 @@ jobs:
           - python-version: "3.7"
           - python-version: "3.8"
           - python-version: "3.9"
-          - python-version: "3.10"
-          - python-version: "3.11"
-          - python-version: "3.12"
 
     steps:
       - uses: actions/checkout@v2
@@ -35,7 +32,7 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
 
-      - name: Install vplanet-private pre-release
+      - name: Install VPLanet
         id: install
         if: steps.setup_python.outcome == 'success'
         shell: bash -l {0}
@@ -44,7 +41,6 @@ jobs:
         run: |
           python -m pip install git+https://[email protected]/VirtualPlanetaryLaboratory/vplanet.git@main#egg=vplanet
 
-
       - name: Install bigplanet
         id: tools
         if: steps.install.outcome == 'success'
@@ -73,7 +69,7 @@ jobs:
           comment_mode: update last
 
       - name: CodeCov
-        uses: codecov/codecov-action@v1.5.0
+        uses: codecov/codecov-action@v2.1.0
         with:
           files: ./coverage.xml
         #shell: bash -l {0}

.gitignore

@@ -21,29 +21,6 @@ SeasonalClimateFiles
 *.csv
 *.md5
 
-#files created from running tests
-tests/Bpstatus/BP_Status/
-tests/Bpstatus/.*
-tests/CreateHDF5/BP_CreateHDF5/
-tests/CreateHDF5/.*
-tests/ExtractArchive/BP_Extract/
-tests/ExtractArchive/.*
-tests/Stats/BP_Stats/
-tests/Stats/.*
-tests/ExtractFilterArchive/BP_Extract/
-tests/ExtractFilterArchive/.*
-tests/ExtractFilterRawData/BP_Extract/
-tests/ExtractFilterRawData/.*
-tests/MD5CheckSum/BP_Extract/
-tests/MD5CheckSum/.*
-tests/UlyssesAggregated/BP_Extract/
-tests/UlyssesAggregated/.*
-tests/UlyssesForward/BP_Extract/
-tests/UlyssesForward/.*
-tests/SingleSim/BP_Extract/
-tests/SingleSim/.*
-
-
 .coverage
 
 # Aux files / build info / garbage
@@ -89,3 +66,4 @@ junit/test-results.xml
 coverage.xml
 tests/UlyssesAggregated/User.csv
 
+htmlcov/

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+exclude: 'docs/'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 21.12b0
+    hooks:
+      - id: black
+        verbose: true
+        exclude: '__init__.py'
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args: ['--profile', 'black']
+        verbose: true
+        exclude: '__init__.py'

README.md

@@ -6,14 +6,15 @@
 
 <p align="center">
   <a href="https://VirtualPlanetaryLaboratory.github.io/bigplanet/"><img src="https://img.shields.io/badge/read-the_docs-blue.svg?style=flat"></a>
-    <img src="https://img.shields.io/badge/Python-3.6--3.10-orange.svg"/></a>
-  <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-purple.svg"/></a>
+  <a href="https://github.com/VirtualPlanetaryLaboratory/bigplanet/actions/workflows/docs.yml">
+  <img src="https://github.com/VirtualPlanetaryLaboratory/bigplanet/actions/workflows/docs.yml/badge.svg">
+    <img src="https://img.shields.io/badge/Python-3.6--3.9-orange.svg"></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-purple.svg"></a>
     <a href="https://github.com/VirtualPlanetaryLaboratory/bigplanet/actions/workflows/tests.yml">
-  <img src="https://github.com/VirtualPlanetaryLaboratory/bigplanet/actions/workflows/tests.yml/badge.svg"/>
-
-
-
+  <img src="https://github.com/VirtualPlanetaryLaboratory/bigplanet/actions/workflows/tests.yml/badge.svg">
+<a href="https://github.com/VirtualPlanetaryLaboratory/bigplanet/actions/workflows/wheels.yml">
+  <img src="https://github.com/VirtualPlanetaryLaboratory/bigplanet/actions/workflows/wheels.yml/badge.svg">
   </a>
 </p>
 
-A suite of data analysis and extraction routines for [VPLanet](https://github.com/VirtualPlanetaryLaboratory/vplanet) and designed to be used with [VSPACE](https://github.com/VirtualPlanetaryLaboratory/vspace) and [MultiPlanet](https://github.com/VirtualPlanetaryLaboratory/multi-planet) scripts. It can also generate files for use with the free version of the [VR Ulysses data explorer](https://www.vrulysses.com/download-ulysses). [Read the docs](https://VirtualPlanetaryLaboratory.github.io/bigplanet/) to learn how to get the most out of your VPLanet parameter sweeps.
+A suite of data analysis and extraction routines for [VPLanet](https://github.com/VirtualPlanetaryLaboratory/vplanet) and designed to be used with [VSPACE](https://github.com/VirtualPlanetaryLaboratory/vspace) and [MultiPlanet](https://github.com/VirtualPlanetaryLaboratory/multi-planet) scripts. It can also generate files for use with the free version of the [VR Ulysses data explorer](https://www.vrulysses.com/download-ulysses). [Read the docs](https://VirtualPlanetaryLaboratory.github.io/bigplanet/) to learn how to get the most out of your `VPLanet` parameter sweeps.

bigplanet/bigplanet.py

@@ -1,19 +1,30 @@
 #!/usr/bin/env python
 
-import os
+import argparse
 import multiprocessing as mp
+import os
 import subprocess as sub
-import argparse
+
 import h5py
 import numpy as np
 import pandas as pd
+
 from .bigplanet_archive import Archive
 from .bigplanet_filter import Filter
-from .bp_get import ReadFile
 from .bp_extract import Md5CheckSum
+from .bp_get import ReadFile
 
 
-def Main(bpInputFile, cores, quiet, overwrite, verbose, archive, deleterawdata, ignorecorrupt):
+def Main(
+    bpInputFile,
+    cores,
+    quiet,
+    overwrite,
+    verbose,
+    archive,
+    deleterawdata,
+    ignorecorrupt,
+):
     # folder,bplArchive,output,bodyFileList,primaryFile,IncludeList,ExcludeList,Ulysses = ReadFile(file,verbose)
     #
     # if if IncludeList != [] and ExcludeList != [] and os.path.isfile(bplArchive) == False:
@@ -23,14 +34,26 @@ def Main(bpInputFile, cores, quiet, overwrite, verbose, archive, deleterawdata,
     #     print("Creating filtered BPF file...")
     #     MainMethodF(bpInputFile,quiet,verbose)
     if deleterawdata == True:
-        #folder_name, bpl_file, outputFile, bodylist, primaryFile, includelist, excludelist, Ulysses, SimName
-        folder, bplArchive, output, bodyFileList, primaryFile, IncludeList, ExcludeList, Ulysses, simname = ReadFile(
-            bpInputFile, verbose, archive)
+        # folder_name, bpl_file, outputFile, bodylist, primaryFile, includelist, excludelist, Ulysses, SimName
+        (
+            folder,
+            bplArchive,
+            output,
+            bodyFileList,
+            primaryFile,
+            IncludeList,
+            ExcludeList,
+            Ulysses,
+            simname,
+        ) = ReadFile(bpInputFile, verbose, archive)
         if os.path.exists(bplArchive) == True:
             Md5CheckSum(bplArchive, ignorecorrupt)
             reply = None
-            question = ("WARNING: This command will delete the " +
-                        folder + " directory along with any MultiPlanet checkpoint files.")
+            question = (
+                "WARNING: This command will delete the "
+                + folder
+                + " directory along with any MultiPlanet checkpoint files."
+            )
             while reply not in ("y", "n"):
                 reply = str(input(question + " (y/n): ")).lower().strip()
                 if reply[:1] == "y":
@@ -42,7 +65,7 @@ def Main(bpInputFile, cores, quiet, overwrite, verbose, archive, deleterawdata,
                 if reply[:1] == "n":
                     print("Files NOT deleted. Exiting.")
                     exit()
-                if reply[:1] != "n" or reply[:1] != "y":
+                else:
                     print("User input was not valid. Exiting.")
                     exit()
 
@@ -60,27 +83,63 @@ def Main(bpInputFile, cores, quiet, overwrite, verbose, archive, deleterawdata,
 def Arguments():
     max_cores = mp.cpu_count()
     parser = argparse.ArgumentParser(
-        description="Extract data from Vplanet simulations")
+        description="Extract data from Vplanet simulations"
+    )
+    parser.add_argument(
+        "bpInputFile", help="Name of the biugplanet input file"
+    )
+    parser.add_argument(
+        "-c",
+        "--cores",
+        type=int,
+        default=max_cores,
+        help="Number of processors used",
+    )
+    parser.add_argument(
+        "-o",
+        "--overwrite",
+        action="store_true",
+        help="overwrite file if it already exists",
+    )
+    parser.add_argument(
+        "-a",
+        "--archive",
+        action="store_true",
+        help="flag for archive file creation",
+    )
+    parser.add_argument(
+        "-deleterawdata",
+        "--deleterawdata",
+        action="store_true",
+        help="removes source files after creation of Bigplanet files",
+    )
     parser.add_argument(
-        "bpInputFile", help="Name of the biugplanet input file")
-    parser.add_argument("-c", "--cores", type=int,
-                        default=max_cores, help="Number of processors used")
-    parser.add_argument("-o", "--overwrite", action="store_true",
-                        help="overwrite file if it already exists")
-    parser.add_argument("-a", "--archive", action="store_true",
-                        help="flag for archive file creation")
-    parser.add_argument("-deleterawdata", "--deleterawdata", action="store_true",
-                        help="removes source files after creation of Bigplanet files")
-    parser.add_argument("-ignorecorrupt", "--ignorecorrupt", action="store_true",
-                        help="ignore data corruption for MD5 Checksum")
+        "-ignorecorrupt",
+        "--ignorecorrupt",
+        action="store_true",
+        help="ignore data corruption for MD5 Checksum",
+    )
     # adds the quiet and verbose as mutually exclusive groups
     group = parser.add_mutually_exclusive_group()
-    group.add_argument("-q", "--quiet", action="store_true",
-                       help="no output for bigplanet")
-    group.add_argument("-v", "--verbose", action="store_true",
-                       help="Prints out excess output for bigplanet")
+    group.add_argument(
+        "-q", "--quiet", action="store_true", help="no output for bigplanet"
+    )
+    group.add_argument(
+        "-v",
+        "--verbose",
+        action="store_true",
+        help="Prints out excess output for bigplanet",
+    )
 
     args = parser.parse_args()
 
-    Main(args.bpInputFile, args.cores, args.quiet,
-         args.overwrite, args.verbose, args.archive, args.deleterawdata, args.ignorecorrupt)
+    Main(
+        args.bpInputFile,
+        args.cores,
+        args.quiet,
+        args.overwrite,
+        args.verbose,
+        args.archive,
+        args.deleterawdata,
+        args.ignorecorrupt,
+    )