diff --git a/.github/workflows/publish-test.yml b/.github/workflows/publish-test.yml
index 2128983..7199b5f 100644
--- a/.github/workflows/publish-test.yml
+++ b/.github/workflows/publish-test.yml
@@ -3,7 +3,7 @@ on:
pull_request:
types: [closed]
paths:
- - 'pandarize/__init__.py'
+ - 'bibReader/__init__.py'
jobs:
deploy:
runs-on: ubuntu-latest
diff --git a/README.md b/README.md
index 913ad3e..18d9b08 100644
--- a/README.md
+++ b/README.md
@@ -1,21 +1,18 @@
-# Pandarize
-This project aims to turn all kinds of data structure/types into a nice tabulated pandas DataFrame
+[![PyPI](https://github.com/jshinm/pandarize/actions/workflows/publish-package.yml/badge.svg)](https://github.com/jshinm/pandarize/actions/workflows/publish-package.yml)
+# bibReader
+The bibReader reads non-standard bib format from files/url and convert them into pandas DataFrames to easily work with the data, and then tranforms them back into a standardized bib file.
# Installation
```
-pip install pandarize
+pip install bibReader
```
# Basic Usage Guide
```python
-from pandarize.frame import Pandarizer
+from bibReader.frame import bReader
-pdr = Pandarizer() #instantiate Pandarizer class
-pdr.load(source='https://somewebsite.com/filename.bib') #it can load from url or local source
-pdr.fit() #infers data types and parse it into pandas dataframe
-pdr.transform() #changes pandas dataframe into different mode of data types
+bib = bReader() #instantiate bReader class
+bib.load(source='https://somewebsite.com/filename.bib') #it can load from url or local source
+bib.fit() #infers data types and parse it into pandas dataframe
+bib.transform() #changes pandas dataframe into different mode of data types
```
-
-# Currently Supported Data Types
-- bib
-
diff --git a/pandarize/__init__.py b/bibReader/__init__.py
similarity index 100%
rename from pandarize/__init__.py
rename to bibReader/__init__.py
diff --git a/pandarize/_util.py b/bibReader/_util.py
similarity index 95%
rename from pandarize/_util.py
rename to bibReader/_util.py
index 78c8df1..ed635db 100644
--- a/pandarize/_util.py
+++ b/bibReader/_util.py
@@ -1,5 +1,6 @@
from datetime import datetime
import re
+import bibReader
def rfindall(string, pattern):
'''Find index of all occurrence of the pattern'''
@@ -62,13 +63,13 @@ def check_url(string):
return False
-def stamper(target, name, url, marker='%'):
+def stamper(target, marker='%'):
'''Creates head stamp on the transformed dataframe
'''
msg = f'{marker}'*60 + '\n'
- msg += f'{marker} This {target} file is created and processed by {name}\n'
+ msg += f'{marker} This {target} file is created and processed by bibReader-{bibReader.__version__}\n'
msg += f'{marker} Date: {datetime.today().date()}\n'
- msg += f'{marker} Webpage: {url}\n'
+ msg += f'{marker} Webpage: https://github.com/jshinm/bibReader/\n'
msg += f'{marker}'*60 + '\n\n'
return msg
diff --git a/pandarize/config/config.yaml b/bibReader/config/config.yaml
similarity index 100%
rename from pandarize/config/config.yaml
rename to bibReader/config/config.yaml
diff --git a/pandarize/frame.py b/bibReader/frame.py
similarity index 97%
rename from pandarize/frame.py
rename to bibReader/frame.py
index 263818a..6c07a6e 100644
--- a/pandarize/frame.py
+++ b/bibReader/frame.py
@@ -3,7 +3,7 @@
from .loader import Loader
from .parser import Parser
-class Pandarizer(Loader, Parser):
+class bReader(Loader, Parser):
def __init__(self):
self.initialize()
diff --git a/pandarize/loader.py b/bibReader/loader.py
similarity index 100%
rename from pandarize/loader.py
rename to bibReader/loader.py
diff --git a/pandarize/parser.py b/bibReader/parser.py
similarity index 100%
rename from pandarize/parser.py
rename to bibReader/parser.py
diff --git a/examples/ndd_member_update.ipynb b/examples/ndd_member_update.ipynb
index da36cbf..ee2e8d6 100644
--- a/examples/ndd_member_update.ipynb
+++ b/examples/ndd_member_update.ipynb
@@ -16,7 +16,7 @@
{
"data": {
"text/plain": [
- "'0.0.8.7'"
+ "'0.0.8.12'"
]
},
"execution_count": 1,
@@ -25,10 +25,10 @@
}
],
"source": [
- "from pandarize.frame import Pandarizer\n",
+ "from bibReader.frame import bReader\n",
"import pandas as pd\n",
- "import pandarize\n",
- "pandarize.__version__"
+ "import bibReader\n",
+ "bibReader.__version__"
]
},
{
@@ -45,8 +45,7 @@
}
],
"source": [
- "pdr = Pandarizer()\n",
- "pdr.initialize()"
+ "bib = bReader()"
]
},
{
@@ -55,8 +54,8 @@
"metadata": {},
"outputs": [],
"source": [
- "pdr.settings['convert_names'] = False\n",
- "pdr.settings['remove_empty_entries'] = False"
+ "bib.settings['convert_names'] = False\n",
+ "bib.settings['remove_empty_entries'] = False"
]
},
{
@@ -65,8 +64,8 @@
"metadata": {},
"outputs": [],
"source": [
- "pdr.load('https://raw.githubusercontent.com/neurodata/neurodata.io/deploy/content/bibs/people.bib')\n",
- "pdr.fit()"
+ "bib.load('https://raw.githubusercontent.com/neurodata/neurodata.io/deploy/content/bibs/people.bib')\n",
+ "bib.fit()"
]
},
{
@@ -186,7 +185,7 @@
"
09/20 – | \n",
" | \n",
" Currently investigating the effect of inductiv... | \n",
- " MS | \n",
+ " MSE | \n",
" BME, JHU | \n",
" staff | \n",
" staffresearch | \n",
@@ -265,7 +264,7 @@
" abstract userb \\\n",
"0 \n",
"1 \n",
- "2 Currently investigating the effect of inductiv... MS \n",
+ "2 Currently investigating the effect of inductiv... MSE \n",
"3 Developed Sparse Projection Oblique Randomer F... MSE \n",
"4 Javier studies how larval zebrafish learn how ... Ph.D. \n",
"\n",
@@ -290,7 +289,7 @@
}
],
"source": [
- "pdr.df.head()"
+ "bib.df.head()"
]
},
{
@@ -299,7 +298,7 @@
"metadata": {},
"outputs": [],
"source": [
- "pdr.df.to_excel(filepath, index=False, engine='xlsxwriter')"
+ "bib.df.to_excel(filepath, index=False, engine='xlsxwriter')"
]
},
{
@@ -315,7 +314,7 @@
"metadata": {},
"outputs": [],
"source": [
- "# pdr.df = pd.read_excel(ufilepath, dtype=object, na_filter=False)"
+ "bib.df = pd.read_excel(ufilepath, dtype=object, na_filter=False)"
]
},
{
@@ -425,13 +424,13 @@
" 09/20 – | \n",
" | \n",
" Currently investigating the effect of inductiv... | \n",
- " MS | \n",
+ " MSE | \n",
" BME, JHU | \n",
" staff | \n",
" staffresearch | \n",
" jshinm | \n",
" jshin69@jhu.edu | \n",
- " | \n",
+ " modrev.org/jshinm | \n",
" safe-zone | \n",
" jong_shin.png | \n",
" 2.0 | \n",
@@ -504,7 +503,7 @@
" abstract userb \\\n",
"0 \n",
"1 \n",
- "2 Currently investigating the effect of inductiv... MS \n",
+ "2 Currently investigating the effect of inductiv... MSE \n",
"3 Developed Sparse Projection Oblique Randomer F... MSE \n",
"4 Javier studies how larval zebrafish learn how ... Ph.D. \n",
"\n",
@@ -518,7 +517,7 @@
" url usere file priority \n",
"0 neurodata.io/about/jovo/ safe-zone vogelstein_joshua.jpg 0.0 \n",
"1 priebe_carey.jpg 1.0 \n",
- "2 safe-zone jong_shin.png 2.0 \n",
+ "2 modrev.org/jshinm safe-zone jong_shin.png 2.0 \n",
"3 tomita_tyler.jpg 3.0 \n",
"4 safe-zone javier_how.jpg 3.0 "
]
@@ -529,26 +528,26 @@
}
],
"source": [
- "pdr.df.head(5)"
+ "bib.df.head(5)"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
- "pdr.df.priority = pdr.df.priority.astype(float)\n",
- "pdr.df.sort_values(['priority'], ascending=True, inplace=True)"
+ "bib.df.priority = bib.df.priority.astype(float)\n",
+ "bib.df.sort_values(['priority'], ascending=True, inplace=True)"
]
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
- "pdr.transform(filename='people')"
+ "bib.transform(filename='people')"
]
},
{
diff --git a/examples/ndd_pubs_update.ipynb b/examples/ndd_pubs_update.ipynb
index e5d4a7f..3e204e7 100644
--- a/examples/ndd_pubs_update.ipynb
+++ b/examples/ndd_pubs_update.ipynb
@@ -16,7 +16,7 @@
{
"data": {
"text/plain": [
- "'0.0.8.7'"
+ "'0.0.8.12'"
]
},
"execution_count": 1,
@@ -25,22 +25,29 @@
}
],
"source": [
- "from pandarize.frame import Pandarizer\n",
- "import pandarize\n",
+ "from bibReader.frame import bReader\n",
"import pandas as pd\n",
- "pandarize.__version__"
+ "import bibReader\n",
+ "bibReader.__version__"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Configuration applied. Please change the setting via .settings as needed.\n"
+ ]
+ }
+ ],
"source": [
- "pdr = Pandarizer()\n",
- "pdr.load('https://raw.githubusercontent.com/neurodata/neurodata.io/deploy/content/bibs/pubs.bib')\n",
- "# pdr.load('pubs.bib') #for local file\n",
- "pdr.fit()"
+ "bib = bReader()\n",
+ "bib.load('https://raw.githubusercontent.com/neurodata/neurodata.io/deploy/content/bibs/pubs.bib')\n",
+ "bib.fit()"
]
},
{
@@ -59,7 +66,7 @@
"metadata": {},
"outputs": [],
"source": [
- "pdr.df.to_excel(filepath, index=False, engine='xlsxwriter')"
+ "bib.df.to_excel(filepath, index=False, engine='xlsxwriter')"
]
},
{
@@ -71,7 +78,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
@@ -106,16 +113,16 @@
" month | \n",
" address | \n",
" ... | \n",
- " adsnote | \n",
+ " elocation-id | \n",
" urldate | \n",
- " tag | \n",
" howpublished | \n",
+ " tag | \n",
+ " note | \n",
+ " day | \n",
" annotation | \n",
" acmid | \n",
" articleno | \n",
" issue_date | \n",
- " note | \n",
- " day | \n",
" \n",
" \n",
" \n",
@@ -126,19 +133,19 @@
],
"text/plain": [
"Empty DataFrame\n",
- "Columns: [type, alias, title, author, author+an, year, keywords, url, month, address, journal, pages, volume, number, booktitle, doi, isbn, abstract, organization, publisher, issn, pmid, numpages, location, series, eprint, archiveprefix, arxivid, editor, chapter, annote, archivePrefix, primaryClass, primaryclass, eprinttype, copyright, URL, elocation-id, shorttitle, eid, adsurl, adsnote, urldate, tag, howpublished, annotation, acmid, articleno, issue_date, note, day]\n",
+ "Columns: [type, alias, title, author, author+an, year, keywords, url, month, address, volume, pages, number, journal, booktitle, doi, isbn, abstract, issn, eprint, archiveprefix, arxivid, chapter, publisher, pmid, annote, numpages, location, series, organization, editor, primaryclass, eprinttype, copyright, shorttitle, archivePrefix, primaryClass, eid, adsurl, adsnote, URL, elocation-id, urldate, howpublished, tag, note, day, annotation, acmid, articleno, issue_date]\n",
"Index: []\n",
"\n",
"[0 rows x 51 columns]"
]
},
- "execution_count": 5,
+ "execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "pdr.df[pdr.df['alias'].duplicated()]"
+ "bib.df[bib.df['alias'].duplicated()]"
]
},
{
@@ -150,16 +157,16 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
- "# pdr.df = pd.read_excel(ufilepath, dtype=object, na_filter=False)"
+ "bib.df = pd.read_excel(ufilepath, dtype=object, na_filter=False)"
]
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
@@ -194,16 +201,16 @@
" month | \n",
" address | \n",
" ... | \n",
- " adsnote | \n",
+ " elocation-id | \n",
" urldate | \n",
- " tag | \n",
" howpublished | \n",
+ " tag | \n",
+ " note | \n",
+ " day | \n",
" annotation | \n",
" acmid | \n",
" articleno | \n",
" issue_date | \n",
- " note | \n",
- " day | \n",
" \n",
" \n",
" \n",
@@ -220,112 +227,112 @@
" 6 | \n",
" OHBM, Rome Italy | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
" \n",
" \n",
" 1 | \n",
" inproceedings | \n",
- " Allen2015synaptome | \n",
- " The Open Synaptome Project: Toward a Microscop... | \n",
- " Smith, Stephen J. and Burns, Randal and Chevil... | \n",
- " 8=highlight | \n",
- " 2015 | \n",
+ " ThomasNeuro2020 | \n",
+ " Automated Neuron Tracing of Sparse Fluorescent... | \n",
+ " Athey, Thomas L and Sulam, Jeremias and Vogels... | \n",
+ " 3=highlight; 1=trainee | \n",
+ " 2020 | \n",
" abspos | \n",
- " https://figshare.com/articles/Open_Synaptome_P... | \n",
- " 10 | \n",
- " Society for Neuroscience, Chicago, IL, USA | \n",
+ " | \n",
+ " 11 | \n",
+ " Neuromatch 3 | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
" 2 | \n",
" inproceedings | \n",
- " XBrain2015 | \n",
- " X-Brain: Quantifying Mesoscale Neuroanatomy Us... | \n",
- " Deyer, Eva L. and Fernandes, Hugo L. and Ronca... | \n",
- " 5=highlight;3=trainee | \n",
- " 2015 | \n",
+ " hayden_naisys_2020 | \n",
+ " A Biological Implementation of Lifelong Learni... | \n",
+ " Vogelstein, Joshua T. and Helm, Hayden and Ped... | \n",
+ " 2=trainee;3=trainee;4=trainee;1=highlight | \n",
+ " 2020 | \n",
" abspos | \n",
- " https://figshare.com/articles/X_Brain_Quantify... | \n",
- " NaN | \n",
- " Figshare | \n",
+ " | \n",
+ " 11 | \n",
+ " NAIsys, Cold Spring Harbor, NY, USA | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
" 3 | \n",
" inproceedings | \n",
- " Design2015 | \n",
- " Optimal Design for Discovery Science: Applicat... | \n",
- " Wang, Shangsi and Yang, Zhi and Zuo, Xi-Nian a... | \n",
- " 1=trainee;7=highlight | \n",
- " 2015 | \n",
+ " berlin_2017 | \n",
+ " Processing and Analyzing Terascale Conjugate A... | \n",
+ " Baden, Alex and Perlman, Eric and Collman, For... | \n",
+ " 1=trainee;5=highlight | \n",
+ " 2017 | \n",
" abspos | \n",
- " https://figshare.com/articles/Optimal_Design_f... | \n",
- " NaN | \n",
- " Figshare | \n",
+ " https://neurodata.io/talks/berlin_2017.pdf | \n",
+ " | \n",
+ " Berlin, Germany | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
" 4 | \n",
" inproceedings | \n",
- " Sparse2015 | \n",
- " A Sparse High Dimensional State-Space Model wi... | \n",
- " Chen, Shaojie and Liu, Kai and Yuguang, Yang a... | \n",
- " 1=trainee;7=highlight | \n",
- " 2015 | \n",
+ " falk_open_data2019 | \n",
+ " NeuroData's Open Data Cloud Ecosystem | \n",
+ " Falk, Benjamin and Vogelstein, Joshua T. | \n",
+ " 2=highlight | \n",
+ " 2019 | \n",
" abspos | \n",
- " https://figshare.com/articles/A_Sparse_High_Di... | \n",
- " NaN | \n",
- " Figshare | \n",
+ " https://neurodata.io/talks/25_NeuroDatas_Open_... | \n",
+ " 7 | \n",
+ " Harvard University, Cambridge, MA, USA | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
"\n",
@@ -335,78 +342,78 @@
"text/plain": [
" type alias \\\n",
"0 inproceedings j12019 \n",
- "1 inproceedings Allen2015synaptome \n",
- "2 inproceedings XBrain2015 \n",
- "3 inproceedings Design2015 \n",
- "4 inproceedings Sparse2015 \n",
+ "1 inproceedings ThomasNeuro2020 \n",
+ "2 inproceedings hayden_naisys_2020 \n",
+ "3 inproceedings berlin_2017 \n",
+ "4 inproceedings falk_open_data2019 \n",
"\n",
" title \\\n",
"0 Clustering Multi-Modal Connectomes \n",
- "1 The Open Synaptome Project: Toward a Microscop... \n",
- "2 X-Brain: Quantifying Mesoscale Neuroanatomy Us... \n",
- "3 Optimal Design for Discovery Science: Applicat... \n",
- "4 A Sparse High Dimensional State-Space Model wi... \n",
+ "1 Automated Neuron Tracing of Sparse Fluorescent... \n",
+ "2 A Biological Implementation of Lifelong Learni... \n",
+ "3 Processing and Analyzing Terascale Conjugate A... \n",
+ "4 NeuroData's Open Data Cloud Ecosystem \n",
"\n",
" author \\\n",
"0 Chung, Jaewon and Pedigo, Benjamin D. and Prie... \n",
- "1 Smith, Stephen J. and Burns, Randal and Chevil... \n",
- "2 Deyer, Eva L. and Fernandes, Hugo L. and Ronca... \n",
- "3 Wang, Shangsi and Yang, Zhi and Zuo, Xi-Nian a... \n",
- "4 Chen, Shaojie and Liu, Kai and Yuguang, Yang a... \n",
+ "1 Athey, Thomas L and Sulam, Jeremias and Vogels... \n",
+ "2 Vogelstein, Joshua T. and Helm, Hayden and Ped... \n",
+ "3 Baden, Alex and Perlman, Eric and Collman, For... \n",
+ "4 Falk, Benjamin and Vogelstein, Joshua T. \n",
"\n",
- " author+an year keywords \\\n",
- "0 1=trainee;2=trainee;4=highlight 2019 abspos \n",
- "1 8=highlight 2015 abspos \n",
- "2 5=highlight;3=trainee 2015 abspos \n",
- "3 1=trainee;7=highlight 2015 abspos \n",
- "4 1=trainee;7=highlight 2015 abspos \n",
+ " author+an year keywords \\\n",
+ "0 1=trainee;2=trainee;4=highlight 2019 abspos \n",
+ "1 3=highlight; 1=trainee 2020 abspos \n",
+ "2 2=trainee;3=trainee;4=trainee;1=highlight 2020 abspos \n",
+ "3 1=trainee;5=highlight 2017 abspos \n",
+ "4 2=highlight 2019 abspos \n",
"\n",
" url month \\\n",
"0 https://figshare.com/articles/Clustering_Multi... 6 \n",
- "1 https://figshare.com/articles/Open_Synaptome_P... 10 \n",
- "2 https://figshare.com/articles/X_Brain_Quantify... NaN \n",
- "3 https://figshare.com/articles/Optimal_Design_f... NaN \n",
- "4 https://figshare.com/articles/A_Sparse_High_Di... NaN \n",
+ "1 11 \n",
+ "2 11 \n",
+ "3 https://neurodata.io/talks/berlin_2017.pdf \n",
+ "4 https://neurodata.io/talks/25_NeuroDatas_Open_... 7 \n",
"\n",
- " address ... adsnote urldate tag \\\n",
- "0 OHBM, Rome Italy ... NaN NaN NaN \n",
- "1 Society for Neuroscience, Chicago, IL, USA ... NaN NaN NaN \n",
- "2 Figshare ... NaN NaN NaN \n",
- "3 Figshare ... NaN NaN NaN \n",
- "4 Figshare ... NaN NaN NaN \n",
+ " address ... elocation-id urldate \\\n",
+ "0 OHBM, Rome Italy ... \n",
+ "1 Neuromatch 3 ... \n",
+ "2 NAIsys, Cold Spring Harbor, NY, USA ... \n",
+ "3 Berlin, Germany ... \n",
+ "4 Harvard University, Cambridge, MA, USA ... \n",
"\n",
- " howpublished annotation acmid articleno issue_date note day \n",
- "0 NaN NaN NaN NaN NaN NaN NaN \n",
- "1 NaN NaN NaN NaN NaN NaN NaN \n",
- "2 NaN NaN NaN NaN NaN NaN NaN \n",
- "3 NaN NaN NaN NaN NaN NaN NaN \n",
- "4 NaN NaN NaN NaN NaN NaN NaN \n",
+ " howpublished tag note day annotation acmid articleno issue_date \n",
+ "0 \n",
+ "1 \n",
+ "2 \n",
+ "3 \n",
+ "4 \n",
"\n",
"[5 rows x 51 columns]"
]
},
- "execution_count": 7,
+ "execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "pdr.df.head(5)"
+ "bib.df.head(5)"
]
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# pdr.df.priority = pdr.df.priority.astype(float)\n",
- "pdr.df.sort_values(['keywords'], ascending=True, inplace=True)"
+ "bib.df.sort_values(['keywords'], ascending=True, inplace=True)"
]
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 10,
"metadata": {},
"outputs": [
{
@@ -441,16 +448,16 @@
" month | \n",
" address | \n",
" ... | \n",
- " adsnote | \n",
+ " elocation-id | \n",
" urldate | \n",
- " tag | \n",
" howpublished | \n",
+ " tag | \n",
+ " note | \n",
+ " day | \n",
" annotation | \n",
" acmid | \n",
" articleno | \n",
" issue_date | \n",
- " note | \n",
- " day | \n",
" \n",
" \n",
" \n",
@@ -467,112 +474,112 @@
" 6 | \n",
" OHBM, Rome Italy | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
" \n",
" \n",
" 1 | \n",
" inproceedings | \n",
- " ThomasNeuro2020 | \n",
- " Automated Neuron Tracing of Sparse Fluorescent... | \n",
- " Athey, Thomas L and Sulam, Jeremias and Vogels... | \n",
- " 3=highlight; 1=trainee | \n",
- " 2020 | \n",
+ " Airan2013 | \n",
+ " Reproducible differentiation of individual of ... | \n",
+ " D, Raag and Vogelstein, Airan A. and Caffo, Jo... | \n",
+ " 2=highlight | \n",
+ " 2013 | \n",
" abspos | \n",
- " NaN | \n",
- " 11 | \n",
- " Neuromatch 3 | \n",
+ " http://dx.doi.org/10.6084/m9.figshare.1284146 | \n",
+ " 4 | \n",
+ " Proc ISMRM, Salt Lake City, UT, USA | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
" 2 | \n",
" inproceedings | \n",
- " hayden_naisys_2020 | \n",
- " A Biological Implementation of Lifelong Learni... | \n",
- " Vogelstein, Joshua T. and Helm, Hayden and Ped... | \n",
- " 2=trainee;3=trainee;4=trainee;1=highlight | \n",
- " 2020 | \n",
+ " Allen2015synaptome | \n",
+ " The Open Synaptome Project: Toward a Microscop... | \n",
+ " Smith, Stephen J. and Burns, Randal and Chevil... | \n",
+ " 8=highlight | \n",
+ " 2015 | \n",
" abspos | \n",
- " NaN | \n",
- " 11 | \n",
- " NAIsys, Cold Spring Harbor, NY, USA | \n",
+ " https://figshare.com/articles/Open_Synaptome_P... | \n",
+ " 10 | \n",
+ " Society for Neuroscience, Chicago, IL, USA | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
" 3 | \n",
" inproceedings | \n",
- " berlin_2017 | \n",
- " Processing and Analyzing Terascale Conjugate A... | \n",
- " Baden, Alex and Perlman, Eric and Collman, For... | \n",
- " 1=trainee;5=highlight | \n",
- " 2017 | \n",
+ " XBrain2015 | \n",
+ " X-Brain: Quantifying Mesoscale Neuroanatomy Us... | \n",
+ " Deyer, Eva L. and Fernandes, Hugo L. and Ronca... | \n",
+ " 5=highlight;3=trainee | \n",
+ " 2015 | \n",
" abspos | \n",
- " https://neurodata.io/talks/berlin_2017.pdf | \n",
- " NaN | \n",
- " Berlin, Germany | \n",
+ " https://figshare.com/articles/X_Brain_Quantify... | \n",
+ " | \n",
+ " Figshare | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
" 4 | \n",
" inproceedings | \n",
- " falk_open_data2019 | \n",
- " NeuroData's Open Data Cloud Ecosystem | \n",
- " Falk, Benjamin and Vogelstein, Joshua T. | \n",
- " 2=highlight | \n",
- " 2019 | \n",
+ " Design2015 | \n",
+ " Optimal Design for Discovery Science: Applicat... | \n",
+ " Wang, Shangsi and Yang, Zhi and Zuo, Xi-Nian a... | \n",
+ " 1=trainee;7=highlight | \n",
+ " 2015 | \n",
" abspos | \n",
- " https://neurodata.io/talks/25_NeuroDatas_Open_... | \n",
- " 7 | \n",
- " Harvard University, Cambridge, MA, USA | \n",
+ " https://figshare.com/articles/Optimal_Design_f... | \n",
+ " | \n",
+ " Figshare | \n",
" ... | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
- " NaN | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
+ " | \n",
"
\n",
" \n",
"\n",
@@ -582,72 +589,72 @@
"text/plain": [
" type alias \\\n",
"0 inproceedings j12019 \n",
- "1 inproceedings ThomasNeuro2020 \n",
- "2 inproceedings hayden_naisys_2020 \n",
- "3 inproceedings berlin_2017 \n",
- "4 inproceedings falk_open_data2019 \n",
+ "1 inproceedings Airan2013 \n",
+ "2 inproceedings Allen2015synaptome \n",
+ "3 inproceedings XBrain2015 \n",
+ "4 inproceedings Design2015 \n",
"\n",
" title \\\n",
"0 Clustering Multi-Modal Connectomes \n",
- "1 Automated Neuron Tracing of Sparse Fluorescent... \n",
- "2 A Biological Implementation of Lifelong Learni... \n",
- "3 Processing and Analyzing Terascale Conjugate A... \n",
- "4 NeuroData's Open Data Cloud Ecosystem \n",
+ "1 Reproducible differentiation of individual of ... \n",
+ "2 The Open Synaptome Project: Toward a Microscop... \n",
+ "3 X-Brain: Quantifying Mesoscale Neuroanatomy Us... \n",
+ "4 Optimal Design for Discovery Science: Applicat... \n",
"\n",
" author \\\n",
"0 Chung, Jaewon and Pedigo, Benjamin D. and Prie... \n",
- "1 Athey, Thomas L and Sulam, Jeremias and Vogels... \n",
- "2 Vogelstein, Joshua T. and Helm, Hayden and Ped... \n",
- "3 Baden, Alex and Perlman, Eric and Collman, For... \n",
- "4 Falk, Benjamin and Vogelstein, Joshua T. \n",
+ "1 D, Raag and Vogelstein, Airan A. and Caffo, Jo... \n",
+ "2 Smith, Stephen J. and Burns, Randal and Chevil... \n",
+ "3 Deyer, Eva L. and Fernandes, Hugo L. and Ronca... \n",
+ "4 Wang, Shangsi and Yang, Zhi and Zuo, Xi-Nian a... \n",
"\n",
- " author+an year keywords \\\n",
- "0 1=trainee;2=trainee;4=highlight 2019 abspos \n",
- "1 3=highlight; 1=trainee 2020 abspos \n",
- "2 2=trainee;3=trainee;4=trainee;1=highlight 2020 abspos \n",
- "3 1=trainee;5=highlight 2017 abspos \n",
- "4 2=highlight 2019 abspos \n",
+ " author+an year keywords \\\n",
+ "0 1=trainee;2=trainee;4=highlight 2019 abspos \n",
+ "1 2=highlight 2013 abspos \n",
+ "2 8=highlight 2015 abspos \n",
+ "3 5=highlight;3=trainee 2015 abspos \n",
+ "4 1=trainee;7=highlight 2015 abspos \n",
"\n",
" url month \\\n",
"0 https://figshare.com/articles/Clustering_Multi... 6 \n",
- "1 NaN 11 \n",
- "2 NaN 11 \n",
- "3 https://neurodata.io/talks/berlin_2017.pdf NaN \n",
- "4 https://neurodata.io/talks/25_NeuroDatas_Open_... 7 \n",
+ "1 http://dx.doi.org/10.6084/m9.figshare.1284146 4 \n",
+ "2 https://figshare.com/articles/Open_Synaptome_P... 10 \n",
+ "3 https://figshare.com/articles/X_Brain_Quantify... \n",
+ "4 https://figshare.com/articles/Optimal_Design_f... \n",
"\n",
- " address ... adsnote urldate tag \\\n",
- "0 OHBM, Rome Italy ... NaN NaN NaN \n",
- "1 Neuromatch 3 ... NaN NaN NaN \n",
- "2 NAIsys, Cold Spring Harbor, NY, USA ... NaN NaN NaN \n",
- "3 Berlin, Germany ... NaN NaN NaN \n",
- "4 Harvard University, Cambridge, MA, USA ... NaN NaN NaN \n",
+ " address ... elocation-id urldate \\\n",
+ "0 OHBM, Rome Italy ... \n",
+ "1 Proc ISMRM, Salt Lake City, UT, USA ... \n",
+ "2 Society for Neuroscience, Chicago, IL, USA ... \n",
+ "3 Figshare ... \n",
+ "4 Figshare ... \n",
"\n",
- " howpublished annotation acmid articleno issue_date note day \n",
- "0 NaN NaN NaN NaN NaN NaN NaN \n",
- "1 NaN NaN NaN NaN NaN NaN NaN \n",
- "2 NaN NaN NaN NaN NaN NaN NaN \n",
- "3 NaN NaN NaN NaN NaN NaN NaN \n",
- "4 NaN NaN NaN NaN NaN NaN NaN \n",
+ " howpublished tag note day annotation acmid articleno issue_date \n",
+ "0 \n",
+ "1 \n",
+ "2 \n",
+ "3 \n",
+ "4 \n",
"\n",
"[5 rows x 51 columns]"
]
},
- "execution_count": 9,
+ "execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "pdr.df.reset_index(drop=True).head(5)"
+ "bib.df.reset_index(drop=True).head(5)"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
- "pdr.transform(filename='pubs')"
+ "bib.transform(filename='pubs')"
]
},
{
diff --git a/setup.py b/setup.py
index 81e7c77..f580921 100644
--- a/setup.py
+++ b/setup.py
@@ -1,20 +1,20 @@
from distutils.core import setup
from setuptools import find_packages
-import pandarize
+import bibReader
-VERSION = pandarize.__version__
+VERSION = bibReader.__version__
with open('README.md', 'r') as f:
README = f.read()
setup(
- name='Pandarize',
+ name='bibReader',
version=VERSION,
author='Jong M. Shin',
author_email='jshinm@gmail.com',
packages=find_packages(),
- package_data = {"": ['pandarize/config/config.yaml']},
+ package_data = {"": ['bibReader/config/config.yaml']},
include_package_data=True,
- url='https://github.com/jshinm/pandarize/',
+ url='https://github.com/jshinm/bibReader/',
license='MIT',
description='Turns data into panda dataframe',
readme='README.md',