Merge pull request #35 from sepandhaghighi/dev

Version 0.6

.travis.yml

@@ -12,10 +12,6 @@ matrix:
           python: 3.6
         - os: linux
           python: 3.5
-        - os: linux
-          python: 3.4
-        - os: linux
-          python: 2.7
         - os: osx
           language: generic
           env: TOXENV=py36
@@ -25,14 +21,19 @@ matrix:
         - os: linux
           python: 3.8-dev
           dist: xenial
+        - os: linux
+          python: 3.9-dev
+          dist: xenial
         - os: linux
           python: nightly
           dist: xenial
     allow_failures:
         - os: linux
-          python: 2.7
+          python: 3.9-dev
+          dist: xenial
         - os: linux
-          python: 3.4
+          python: nightly
+          dist: xenial
 install:
   - chmod +x .travis/install.sh
   - .travis/install.sh

CHANGELOG.md

@@ -5,6 +5,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+## [0.6] - 2020-07-24
+### Added
+- Matrix Market format
+### Changed
+- `json_maker` function optimized
+- `dl_maker` function optimized
+- `tgf_maker` function optimized
+- `lp_maker` function optimized
 ## [0.5] - 2020-07-01
 ### Added
 - TSV format
@@ -57,7 +65,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - JSON format
 - README
 
-[Unreleased]: https://github.com/sepandhaghighi/pyrgg/compare/v0.5...dev
+[Unreleased]: https://github.com/sepandhaghighi/pyrgg/compare/v0.6...dev
+[0.6]: https://github.com/sepandhaghighi/pyrgg/compare/v0.5...v0.6
 [0.5]: https://github.com/sepandhaghighi/pyrgg/compare/v0.4...v0.5
 [0.4]: https://github.com/sepandhaghighi/pyrgg/compare/v0.3...v0.4
 [0.3]: https://github.com/sepandhaghighi/pyrgg/compare/v0.2...v0.3

README.md

@@ -90,23 +90,23 @@ Pyrgg target audiences are computer scientists who study graph algorithms and gr
 ## Installation		
 
 ### Source Code
-- Download [Version 0.5](https://github.com/sepandhaghighi/pyrgg/archive/v0.5.zip) or [Latest Source ](https://github.com/sepandhaghighi/pyrgg/archive/dev.zip)
+- Download [Version 0.6](https://github.com/sepandhaghighi/pyrgg/archive/v0.6.zip) or [Latest Source ](https://github.com/sepandhaghighi/pyrgg/archive/dev.zip)
 - `pip install -r requirements.txt` or `pip3 install -r requirements.txt` (Need root access)
 - `python3 setup.py install` or `python setup.py install` (Need root access)				
 
 ### PyPI
 
 - Check [Python Packaging User Guide](https://packaging.python.org/installing/)     
-- `pip install pyrgg==0.5` or `pip3 install pyrgg==0.5` (Need root access)							
+- `pip install pyrgg==0.6` or `pip3 install pyrgg==0.6` (Need root access)							
 
 ### Conda
 
 - Check [Conda Managing Package](https://conda.io)
 - `conda install -c sepandhaghighi pyrgg` (Need root access)	
 
 ### Exe Version (Only Windows)
-- Download [Exe-Version 0.5](https://github.com/sepandhaghighi/pyrgg/releases/download/v0.5/PYRGG-0.5.exe)
-- Run `PYRGG-0.5.exe`
+- Download [Exe-Version 0.6](https://github.com/sepandhaghighi/pyrgg/releases/download/v0.6/PYRGG-0.6.exe)
+- Run `PYRGG-0.6.exe`
 
 ### System Requirements
 Pyrgg will likely run on a modern dual core PC. Typical configuration is:
@@ -184,6 +184,8 @@ or send an email to [[email protected]](mailto:[email protected] "[email protected]").
 - [Sample 2-TGF](https://www.dropbox.com/s/9mjeq4w973189cc/1000.tgf?dl=0) (1000 Vertices , 61KB)
 - [Sample 1-UCINET DL](https://www.dropbox.com/s/82wrl86uowwjud2/100.dl?dl=0) (100 Vertices , 8KB)
 - [Sample 2-UCINET DL](https://www.dropbox.com/s/kbzbsy47uvfqdsi/1000.dl?dl=0) (1000 Vertices , 729KB)
+- [Sample 1-MTX](https://www.dropbox.com/s/ztw3vg0roups82q/100.mtx?dl=0) (100 Vertices , 59KB)
+- [Sample 2-MTX](https://www.dropbox.com/s/skjjvbbzrpvryl4/1000.mtx?dl=0) (1000 Vertices , 1.8MB)
 
 
 
@@ -208,7 +210,7 @@ or send an email to [[email protected]](mailto:[email protected] "[email protected]").
 
 - [DIMACS(.gr)](http://www.diag.uniroma1.it/challenge9/format.shtml)
 	```
-		p sp <number of vertices> <number of directed edge>
+		p sp <number of vertices> <number of edges>
 		a <head_1> <tail_1> <weight_1>
 
 		.
@@ -351,6 +353,16 @@ or send an email to [[email protected]](mailto:[email protected] "[email protected]").
 		.
 		n k weight_n	
 	```
+- [Matrix Market(.mtx)](https://math.nist.gov/MatrixMarket/formats.html)
+   ```
+	   %%MatrixMarket matrix coordinate real general
+       <number of vertices>  <number of vertices>  <number of edges>
+       <head_1>    <tail_1>    <weight_1> 
+       .
+       .
+       .
+       <head_n>    <tail_n>    <weight_n> 
+   ```
 - [Pickle(.p)](https://docs.python.org/3.5/library/pickle.html) (Binary Format)	
 
 

codecov.yml

@@ -9,3 +9,6 @@ coverage:
     patch:
       default:
         enabled: no
+    project:
+      default:
+        threshold: 1%

dev-requirements.txt

@@ -1,6 +1,7 @@
 art==4.7
 pyyaml==5.3.1
 codecov>=2.0.15
+scipy>=1.2.0
 pytest>=4.3.1
 pytest-cov>=2.6.1
 setuptools>=40.8.0

otherfile/Version.rc

@@ -1,7 +1,7 @@
 VSVersionInfo(
   ffi=FixedFileInfo(
-    filevers=(0, 5, 0, 0),
-    prodvers=(0, 5, 0, 0),
+    filevers=(0, 6, 0, 0),
+    prodvers=(0, 6, 0, 0),
     mask=0x3f,
     flags=0x0,
     OS=0x40004,
@@ -16,12 +16,12 @@ VSVersionInfo(
         u'040904B0',
         [StringStruct(u'CompanyName', u'Sepand Haghighi'),
         StringStruct(u'FileDescription', u'PYRGG.exe'),
-        StringStruct(u'FileVersion', u'0.5.0.0'),
+        StringStruct(u'FileVersion', u'0.6.0.0'),
         StringStruct(u'InternalName', u'PYRGG.exe'),
         StringStruct(u'LegalCopyright', u'Copyright (c) 2020 Sepand Haghighi'),
         StringStruct(u'OriginalFilename', u'PYRGG.exe'),
         StringStruct(u'ProductName', u'PYRGG'),
-        StringStruct(u'ProductVersion', u'0, 5, 0, 0')])
+        StringStruct(u'ProductVersion', u'0, 6, 0, 0')])
     ]), 
     VarFileInfo([VarStruct(u'Translation', [1033, 1200])])
   ]

otherfile/version_check.py

@@ -4,7 +4,7 @@
 import sys
 import codecs
 Failed = 0
-VERSION = "0.5"
+VERSION = "0.6"
 
 VERSION_1 = VERSION.split(".")[0]
 VERSION_2 = str(int(float(VERSION) * 10 - int(VERSION_1) * 10))

pyrgg/__main__.py

@@ -17,7 +17,8 @@
     7: json_maker,
     8: dl_maker,
     9: tgf_maker,
-    10: tsv_maker}
+    10: tsv_maker,
+    11: mtx_maker}
 
 
 def run():

pyrgg/params.py

@@ -4,8 +4,8 @@
 
 MENU_ITEMS1 = {
     "file_name": "File Name : ",
-    "output_format": "Graph Format : \nDIMACS(.gr)[1] | JSON(.json)[2] | CSV(.csv)[3] | YAML(.yaml)[4]\n| WEL(.wel)[5] | ASP(.lp)[6] | Pickle(.p)[7] | UCINET DL Format(.dl)[8] | TGF(.tgf)[9] | TSV("
-                     ".tsv)[10]",
+    "output_format": "Graph Formats : \n1- DIMACS(.gr)\n2- JSON(.json)\n3- CSV(.csv)\n4- YAML(.yaml)\n5- WEL(.wel)\n6- ASP(.lp)\n7- Pickle(.p)\n8- UCINET DL(.dl)\n9- TGF(.tgf)\n10- TSV("
+                     ".tsv)\n11- Matrix Market(.mtx)\n",
     "weight": "Weighted[1] or Unweighted[2]"}
 
 MENU_ITEMS2 = {"vertices": "Vertices Number : ",
@@ -29,10 +29,11 @@
     7: ".p",
     8: ".dl",
     9: ".tgf",
-    10: ".tsv"}
+    10: ".tsv",
+    11: ".mtx"}
 
 
-PYRGG_VERSION = "0.5"
+PYRGG_VERSION = "0.6"
 
 SOURCE_DIR = os.getcwd()
 

pyrgg/pyrgg.py

@@ -208,7 +208,7 @@ def input_filter(input_dict):
         filtered_dict["self_loop"] = 1
     if filtered_dict["multigraph"] not in [1, 2]:
         filtered_dict["multigraph"] = 1
-    if filtered_dict["output_format"] not in list(range(1, 11)):
+    if filtered_dict["output_format"] not in list(range(1, 12)):
         filtered_dict["output_format"] = 1
     return filtered_dict
 
@@ -565,19 +565,34 @@ def json_maker(
     edge_dic = dicts[0]
     weight_dic = dicts[1]
     edge_number = dicts[2]
+    first_line = True
     nodes = '\t\t\t"nodes":[\n'
     edges = '\t\t\t"edges":[\n'
+    file.write('{\n\t"graph": {\n')
+    file.write(nodes)
     for i in edge_dic.keys():
+        nodes = ""
+        if first_line:
+            first_line = False
+        else:
+            nodes += ",\n"
         nodes = nodes + '\t\t\t{\n\t\t\t\t' + \
-            '"id": ' + '"' + str(i) + '"\n\t\t\t},\n'
+            '"id": ' + '"' + str(i) + '"\n\t\t\t}'
+        file.write(nodes)
+    file.write("\n\t\t],\n")
+    first_line = True
+    file.write(edges)
+    for i in edge_dic.keys():
         for j, value in enumerate(edge_dic[i]):
+            edges = ""
+            if first_line:
+                first_line = False
+            else:
+                edges += ",\n"
             edges = edges + '\t\t\t{\n\t\t\t\t"source": ' + '"' + str(i) + '",\n\t\t\t\t' + '"target": ' + '"' + str(
-                value) + '",\n\t\t\t\t' + '"weight": ' + '"' + str(weight_dic[i][j]) + '"\n\t\t\t},\n'
-    nodes = nodes[:-2] + "\n\t\t],\n"
-    edges = edges[:-2] + "\n\t\t]\n\t}\n}"
-    file.write('{\n\t"graph": {\n')
-    file.write(nodes)
-    file.write(edges)
+                value) + '",\n\t\t\t\t' + '"weight": ' + '"' + str(weight_dic[i][j]) + '"\n\t\t\t}'
+            file.write(edges)
+    file.write("\n\t\t]\n\t}\n}")
     file.close()
     return edge_number
 
@@ -794,6 +809,69 @@ def wel_maker(
     return edge_number
 
 
+def mtx_maker(
+        file_name,
+        min_weight,
+        max_weight,
+        vertices,
+        min_edge,
+        max_edge,
+        sign,
+        direct,
+        self_loop,
+        multigraph):
+    """
+    Create output file in Matrix Market format.
+
+    :param file_name: file name
+    :type file_name: str
+    :param min_weight: weight min range
+    :type min_weight: int
+    :param max_weight: weight max range
+    :type max_weight: int
+    :param vertices: number of vertices
+    :type vertices: int
+    :param min_edge : minimum edge number
+    :type min_edge : int
+    :param max_edge : maximum edge number
+    :type max_edge : int
+    :param sign: weight sign flag
+    :type sign: int
+    :param direct: directed and undirected graph flag
+    :type direct: int
+    :param self_loop: self loop flag
+    :type self_loop: int
+    :param multigraph: multigraph flag
+    :type multigraph: int
+    :return: edge_number as int
+    """
+    file = open(file_name + ".mtx", "w")
+    dicts = edge_gen(
+        vertices,
+        min_weight,
+        max_weight,
+        min_edge,
+        max_edge,
+        sign,
+        direct,
+        self_loop,
+        multigraph)
+    edge_dic = dicts[0]
+    weight_dic = dicts[1]
+    edge_number = dicts[2]
+    max_edge_length = len(str(vertices))
+    file.write("%%MatrixMarket matrix coordinate real general\n")
+    file.write("{0}    {0}    {1}\n".format(str(vertices), str(edge_number)))
+    for i in edge_dic.keys():
+        for j, value in enumerate(edge_dic[i]):
+            shift1 = (max_edge_length - len(str(i))) + 4
+            shift2 = (max_edge_length - len(str(value))) + 4
+            file.write(str(i) + shift1 * " " + str(value) + shift2 * " " +
+                       str(weight_dic[i][j]) + "\n")
+    file.close()
+    return edge_number
+
+
 def lp_maker(
         file_name,
         min_weight,
@@ -844,15 +922,12 @@ def lp_maker(
     edge_dic = dicts[0]
     weight_dic = dicts[1]
     edge_number = dicts[2]
-    nodes = ''
-    edges = ''
     for i in edge_dic.keys():
-        nodes = nodes + 'node(' + str(i) + ").\n"
+        file.write('node(' + str(i) + ").\n")
+    for i in edge_dic.keys():
         for j, value in enumerate(edge_dic[i]):
-            edges = edges + \
-                'edge(' + str(i) + "," + str(value) + "," + str(weight_dic[i][j]) + ").\n"
-    file.write(nodes)
-    file.write(edges)
+            file.write('edge(' + str(i) + "," + str(value) +
+                       "," + str(weight_dic[i][j]) + ").\n")
     file.close()
     return edge_number
 
@@ -907,16 +982,13 @@ def tgf_maker(
     edge_dic = dicts[0]
     weight_dic = dicts[1]
     edge_number = dicts[2]
-    nodes = ''
-    edges = ''
     for i in edge_dic.keys():
-        nodes = nodes + str(i) + "\n"
-        for j, value in enumerate(edge_dic[i]):
-            edges = edges + str(i) + " " + str(value) + \
-                " " + str(weight_dic[i][j]) + "\n"
-    file.write(nodes)
+        file.write(str(i) + "\n")
     file.write("#\n")
-    file.write(edges)
+    for i in edge_dic.keys():
+        for j, value in enumerate(edge_dic[i]):
+            file.write(str(i) + " " + str(value) + " " +
+                       str(weight_dic[i][j]) + "\n")
     file.close()
     return edge_number
 
@@ -971,13 +1043,11 @@ def dl_maker(
     edge_dic = dicts[0]
     weight_dic = dicts[1]
     edge_number = dicts[2]
-    edges = ''
+    file.write("dl\nformat=edgelist1\nn=" + str(vertices) + "\ndata:\n")
     for i in edge_dic.keys():
         for j, value in enumerate(edge_dic[i]):
-            edges = edges + str(i) + " " + str(value) + \
-                " " + str(weight_dic[i][j]) + "\n"
-    file.write("dl\nformat=edgelist1\nn=" + str(vertices) + "\ndata:\n")
-    file.write(edges)
+            file.write(str(i) + " " + str(value) + " " +
+                       str(weight_dic[i][j]) + "\n")
     file.close()
     return edge_number