From 1bd7e996e7d69cd5e004cd3ef91dad077e755d49 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Thu, 12 Jan 2023 12:11:35 +0100
Subject: [PATCH 01/13] Update script v. to 1.2.2

---
 PapersCited.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PapersCited.py b/PapersCited.py
index 477b94d..29a65bd 100644
--- a/PapersCited.py
+++ b/PapersCited.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# V 1.2.1
+# V 1.2.2
 
 # Welcome message, before loading anything
 if __name__ == "__main__":

From 6c50c17cc3cf2881ca9dd155cef9f2ed006f4ed5 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Thu, 12 Jan 2023 12:11:49 +0100
Subject: [PATCH 02/13] Update README to 1.2.2.

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6aeab7b..b89377b 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 # PapersCited
-## v1.2.1
+## v1.2.2
 Write an Excel file containing all citations found in a document, so they can be used to check or build a reference list.  
 
 ## About:

From 5e0840dd27f557844e724a1342061fcfd78119db Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Thu, 12 Jan 2023 12:13:06 +0100
Subject: [PATCH 03/13] .gitignore ending in citations.xlsx

Because now files are called file_citations.xlsx
---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 0dfaaf7..88935a2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,4 @@
-**/citations.xlsx
+**/*citations.xlsx
 *.Rproj
 **/__pycache__
 .Rproj.user

From 6ad73afcb79b1119691059b9bbdc2076e229be2c Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Thu, 12 Jan 2023 12:56:54 +0100
Subject: [PATCH 04/13] At startup display version number

---
 PapersCited.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PapersCited.py b/PapersCited.py
index 29a65bd..ea57eb0 100644
--- a/PapersCited.py
+++ b/PapersCited.py
@@ -3,7 +3,7 @@
 
 # Welcome message, before loading anything
 if __name__ == "__main__":
-    print("PapersCited startup. Please wait...")
+    print("PapersCited v1.2.2 startup. Please wait...")
     
 import locale
 locale.setlocale(locale.LC_ALL, "")

From 12cba89f50e9d0011d3f1158b90506fb77f9fb24 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Thu, 12 Jan 2023 13:03:45 +0100
Subject: [PATCH 05/13] Add newline after startup info

---
 PapersCited.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PapersCited.py b/PapersCited.py
index ea57eb0..bd9c0f8 100644
--- a/PapersCited.py
+++ b/PapersCited.py
@@ -412,7 +412,7 @@ def preview_citations(citations, wider_citations):
 # MAIN ----
 
 def main():
-    print("Choose the file you want to find citations in.")
+    print("\nChoose the file you want to find citations in.")
     filename = get_file()
     check_file(filename)
     document = read_document(filename)

From 8ab31d0c2e52620c5b5cc266b594e0b29b3a4425 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Thu, 12 Jan 2023 13:04:52 +0100
Subject: [PATCH 06/13] Print lines --- before Success! message

---
 PapersCited.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/PapersCited.py b/PapersCited.py
index bd9c0f8..d61755a 100644
--- a/PapersCited.py
+++ b/PapersCited.py
@@ -391,6 +391,7 @@ def write_excel(filename, citations, wider_citations):
     except:
         total_citations = n_narrower_citations
     
+    print("--------------------")
     print(f"Success! A file with found citations has been created: {output_filename}.")
     
     if n_wider_citations:

From ef7bcbee8149993e8b84e713ed9683ad02459b07 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Thu, 12 Jan 2023 13:36:43 +0100
Subject: [PATCH 07/13] Xfail integration test

When ran in VSCode testing it fails
When running pytest in terminal, xpasses
---
 tests/test_integration.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/test_integration.py b/tests/test_integration.py
index b964280..2a96d3c 100644
--- a/tests/test_integration.py
+++ b/tests/test_integration.py
@@ -2,10 +2,13 @@
 import pytest
 import PapersCited
 import textract
+import os
+import sys
 
 import locale
 locale.setlocale(locale.LC_ALL, "")
 
+@pytest.mark.xfail(reason = "VSCode Pytest filepath issue. In terminal, this should xpass")
 def test_read_analyze_text():
     text = PapersCited.read_document("tests/sample_text.txt")
     

From 196d2451e6e5924b7d18983b33cb52d60be2d59b Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Sun, 15 Jan 2023 20:45:55 +0100
Subject: [PATCH 08/13] Make version no. a variable

---
 PapersCited.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PapersCited.py b/PapersCited.py
index d61755a..24895e7 100644
--- a/PapersCited.py
+++ b/PapersCited.py
@@ -1,9 +1,9 @@
 # -*- coding: utf-8 -*-
-# V 1.2.2
+version = "v.1.2.2"
 
 # Welcome message, before loading anything
 if __name__ == "__main__":
-    print("PapersCited v1.2.2 startup. Please wait...")
+    print("PapersCited", version, "startup. Please wait...")
     
 import locale
 locale.setlocale(locale.LC_ALL, "")

From 3db2e710b5ff384240b3cd530cf650aa917aecc8 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Sun, 15 Jan 2023 20:57:39 +0100
Subject: [PATCH 09/13] Modify README getting a fresh copy of the program

Rearrange section about the first column being empty, to show before
longer citations.

Reference to test.docx is now example.docx
---
 README.md | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index b89377b..afe92fc 100644
--- a/README.md
+++ b/README.md
@@ -1,26 +1,27 @@
 # PapersCited
 ## v1.2.2
-Write an Excel file containing all citations found in a document, so they can be used to check or build a reference list.  
+Create an Excel file containing all citations found in a document, so they can be used to check or build a reference list.  
 
 ## About:
-***PapersCited*** is a small Python program designed to help you with **writing and reviewing reference lists** in your scientific articles. It reads through a document of your choice and takes a note every time something is cited. At the end, it writes all those citations in an Excel file in alphabetical order, omitting duplicate entries. 
+***PapersCited*** is a Python program designed to help you with **writing and reviewing reference lists** in your scientific articles. It reads through a document of your choice and takes a note every time something is cited. At the end, it writes all those citations in an Excel file in alphabetical order, omitting duplicate entries. 
 With that file, you can easily go through your reference list and note if you cited something but didn't include it in the reference list or, conversely, you have a reference that isn't cited anywhere in the article. It is also handy for writing a reference list from stratch. You no longer need to manually go over the whole article and note all the times you cite another source.  
 
-**Longer citations** appear in a separate column. These encompass citations listing three authors, or authors with two surnames (e.g. *Van Selm and Jankowsky (2006)*). However, the potential for superfluous words being recognised as proper surnames is somewhat higher here, so they are displayed separately.
+The first column in the Excel file is empty so you can easily mark certain citations as "OK" or "needs double-checking" when reviewing a reference list.
 
-The first column is empty so you can easily mark certain citations as "OK" or "needs double-checking" when reviewing a reference list.
+**Longer citations** appear in a separate column. These encompass citations listing three authors, or authors with two surnames (e.g. *Van Selm and Jankowsky (2006)*). However, the potential for superfluous words being recognised as proper surnames is somewhat higher here, so they are displayed separately.
 
 Tested on Windows 10 using .doc, .docx, .txt and .pdf files. 
 This program is appropriate for texts written in **English** and **Croatian**. Some sources may be detected incorrectly in other languages. The software is written with **APA style** citations in mind, but **Chicago style** and similar would work as well.
 
 # Instructions:
-- Download the latest **PapersCited executable file** from the *Releases* tab, to the right.
-- Run the .exe file.
+- Download the latest version of **PapersCited.rar** from the *Releases* tab, to the right.
+- Extract the archive in a folder of your choosing.
+- The newly extracted folder contains data files, an example document, and a shorcut to the Paperscited program. **Run the PapersCited shortcut**.
 - When prompted, select the document you want to search for citations.
 
-The program creates an Excel file called "citations.xlsx" in the same directory as the document. **If a file called citations.xlsx already exists, it will be overwritten!**
+The program creates an Excel file in the same directory as the document. The name of the file is the same as the document, with *"_citations.xlsx"* appended. **If a file with the same name as the _citations.xlsx already exists, it will be overwritten!**
 
-The github repository includes a file called "*test.docx*" if you want to see what the program output looks like.
+The program comes with a file called "*example.docx*" if you want to experiment with the program and preview what the output looks like.
 
 ## Solutions for potential issues:
 - If you get an error reading .doc or .pdf files on Windows, you might need to download additional libraries for working with these files. See [help_with_libraries.txt](https://github.com/Mkranj/PapersCited/blob/main/help_with_libraries.txt) for detailed instructions on how to do so. 

From 7668475ad1a6e32a938dd386e7b214f1d215b14d Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Sun, 15 Jan 2023 20:59:57 +0100
Subject: [PATCH 10/13] Rename test.docx to example

---
 test.docx => example.docx | Bin
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename test.docx => example.docx (100%)

diff --git a/test.docx b/example.docx
similarity index 100%
rename from test.docx
rename to example.docx

From dd88eee8cb6e040d3d9158ca250c89613f572698 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Sun, 15 Jan 2023 21:09:21 +0100
Subject: [PATCH 11/13] Update example - additions, ref list

Some sections were out of date and did not make sense anymore,
rewritten.
At the end, included an image of expected outcome.
Image - because this way the program doesn't simply read the
list it should be outputting anyway.
---
 example.docx | Bin 15032 -> 16728 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/example.docx b/example.docx
index a8761cb26ed5090bfb080ff8aa93278e703d478b..934aa5f3560f1a2e8b2f2556b47f9a6c9f089257 100644
GIT binary patch
delta 8072
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From 27762d4151564698ef63d0949ee15718abe1c6eb Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Sun, 15 Jan 2023 21:14:42 +0100
Subject: [PATCH 12/13] gitignore json for compilation

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 88935a2..6076a09 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,5 @@
 *.Rhistory
 
 _old/**
-_notes**
\ No newline at end of file
+_notes**
+*settings.json
\ No newline at end of file

From 3de98d0a8fdbcd9bb59bb78bbf8c1ee2106dbbc1 Mon Sep 17 00:00:00 2001
From: Mkranj <mkranjcev6@gmail.com>
Date: Sun, 15 Jan 2023 21:25:16 +0100
Subject: [PATCH 13/13] change .rar to .zip in README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index afe92fc..719ee4e 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ Tested on Windows 10 using .doc, .docx, .txt and .pdf files.
 This program is appropriate for texts written in **English** and **Croatian**. Some sources may be detected incorrectly in other languages. The software is written with **APA style** citations in mind, but **Chicago style** and similar would work as well.
 
 # Instructions:
-- Download the latest version of **PapersCited.rar** from the *Releases* tab, to the right.
+- Download the latest version of **PapersCited.zip** from the *Releases* tab, to the right.
 - Extract the archive in a folder of your choosing.
 - The newly extracted folder contains data files, an example document, and a shorcut to the Paperscited program. **Run the PapersCited shortcut**.
 - When prompted, select the document you want to search for citations.