Adds two new options + several fixes

README.md

@@ -1,46 +1,50 @@
 flatex.py 
 ---------
 
-This "flattens" a LaTeX document by replacing all \input{X} lines w/ the text actually contained in X. 
-I recently re-factored it to use the `click` module to create a command line interface. 
+This "flattens" a LaTeX document by replacing all `\input{X}` lines with the text actually contained in X. It uses the `click` module to create a command line interface. 
 
-Copyright, 2015, John J. Horton (john.joseph.horton@gmail.com)
-Distributed under the terms of the GNU General Public License
-See http://www.gnu.org/licenses/gpl.txt for details. 
-
-It was inspired by: 
-http://tex.stackexchange.com/questions/21838/replace-inputfilex-by-the-content-of-filex-automatically/21840#21840
+Two new options are available:
+- Specify a .tex subfolder for input files similarly to what the `input@path` command does in the main file
+- Launch an interactive session to allow the user to select only specific sections to import
 
-There are C and perl versions of this, but I wanted a pure python version to fit in w/ my existing paper-creating toolchain.  
+It was inspired by [this discussion on Stack Overflow](http://tex.stackexchange.com/questions/21838/replace-inputfilex-by-the-content-of-filex-automatically/21840#21840). There are C and perl versions of this, but I wanted a pure python version to fit in with my existing paper-creating toolchain.  
 
 To install
 ----------
-    git clone git@github.com:johnjosephhorton/flatex.git
+    git clone https://github.com/johnjosephhorton/flatex.git
     cd flatex
     pip install --editable . 
 
-To use as a stand-alone script
+Usage
 -----------------------------
+As a stand-alone script:
+
     flatex inputfile.tex outputfile.tex
 
-If you want to include the bbl file as well
---------------------------------------------
+If you want to include the bbl file as well:
 
     flatex --include_bbl inputfile.tex outputfile.tex
 
+If you want to specify a .tex subfolder: 
 
-Limitations: 
-------------
+    flatex inputfile.tex outputfile.tex --tex_folder folder_name
+
+If you want to select only specific input files to expand:
 
-1) It doesn't do \includes - just inputs. 
+    flatex inputfile.tex outputfile.tex --interactive
 
-2) I haven't tested it for nested inputs (thought it's designed
-to work on files like). 
 
-3) I haven't tested it for  more complicated file arrangements 
-  e.g., realtive reference inputs that are more complex that just 
-  a file living in the same directory. 
 
-4) The test case writes to the /tmp folder - so the test probably
+Limitations: 
+------------
+
+1. It does also recognize `\includes` commands, but this has not been tested. 
+1. Tested for nested inputs, although not extensively (only two levels deep). 
+1. Tested for file living in subdirectories, only one level deep. 
+1. The test case writes to the /tmp folder - so the test probably
    wouldn't work on Windows(?). 
 
+
+Copyright, 2015, John J. Horton (john.joseph.horton@gmail.com)
+Distributed under the terms of the GNU General Public License
+See http://www.gnu.org/licenses/gpl.txt for details. 

flatex.py

@@ -1,16 +1,19 @@
-import click
 import os
 import re
-import sys
+import click
 
-def is_input(line):
+def is_input(line, include_too=True):
     """
-    Determines whether or not a read in line contains an uncommented out
-    \input{} statement. Allows only spaces between start of line and
-    '\input{}'.
+    Determines via regex whether or not a line from file contains an
+    uncommented \\input{} statement. Allows only spaces between start
+    of line and '\\input{}'.
     """
-    #tex_input_re = r"""^\s*\\input{[^}]*}""" # input only
-    tex_input_re = r"""(^[^\%]*\\input{[^}]*})|(^[^\%]*\\include{[^}]*})"""  # input or include
+    if include_too:
+        # input or include (not tested)
+        tex_input_re = r"""(^[^\%]*\\input{[^}]*})|(^[^\%]*\\include{[^}]*})"""
+    else:
+        # input only
+        tex_input_re = r"""^\s*\\input{[^}]*}"""
     return re.search(tex_input_re, line)
 
 
@@ -19,44 +22,73 @@ def get_input(line):
     Gets the file name from a line containing an input statement.
     """
     tex_input_filename_re = r"""{[^}]*"""
-    m = re.search(tex_input_filename_re, line)
-    return m.group()[1:]
+    matched_text = re.search(tex_input_filename_re, line)
+    return matched_text.group()[1:]
 
 
-def combine_path(base_path, relative_ref):
+def combine_path(base_path, relative_ref, tex_folder):
     """
     Combines the base path of the tex document being worked on with the
     relate reference found in that document.
+
+    Use specific .tex folder if provided by the user.
     """
-    if (base_path != ""):
+    if base_path:
         os.chdir(base_path)
+    # avoid duplicating tex_folder
+    if tex_folder and tex_folder in relative_ref:
+        tex_folder = ''
     # Handle if .tex is supplied directly with file name or not
     if relative_ref.endswith('.tex'):
-        return os.path.join(base_path, relative_ref)
+        return os.path.join(base_path, tex_folder, relative_ref)
     else:
-        return os.path.abspath(relative_ref) + '.tex'
+        return os.path.abspath(os.path.join(tex_folder, relative_ref))+'.tex'
 
 
-def expand_file(base_file, current_path, include_bbl, noline):
+def expand_file(base_file, current_path, include_bbl, noline, tex_folder, interactive):
     """
-    Recursively-defined function that takes as input a file and returns it
-    with all the inputs replaced with the contents of the referenced file.
+    Recursively-defined function that:
+    - takes as input a file and opens it
+    - looks for 'input' or 'include' commands and get their file references
+    - analyze the references for further commands (recursively)
+    - then expands their content inside the main tex, appending it
+    - and return the complete file
+
+    With the interactive option the user is allowed to chose which file to
+    expand (if maybe some section are still worked on, or don't need to be added.)
     """
     output_lines = []
-    f = open(base_file, "r")
-    for line in f:
-        if is_input(line):
-            new_base_file = combine_path(current_path, get_input(line))
-            output_lines += expand_file(new_base_file, current_path, include_bbl, noline)
-            if noline:
-                pass
+    with open(base_file, "r") as file_to_read:
+        for line in file_to_read:
+            bbl_flag = (
+                line.startswith("\\bibliography")
+                and (not line.startswith("\\bibliographystyle")))
+            if is_input(line):
+                input_str = get_input(line)
+                if interactive:
+                    prompt_q = "Expand this section (Y or yes to proceed)?\n {}\n".format(input_str)
+                    user_input = raw_input(prompt_q) # Python 3 incompatibility
+                    user_input = user_input.lower()
+                    proceed = True if (
+                        user_input == 'y' or user_input == 'yes') else False
+                else:
+                    proceed = True
+                if proceed:
+                    new_base_file = combine_path(current_path, input_str, tex_folder)
+                    output_lines += expand_file(
+                        new_base_file, current_path, include_bbl,
+                        noline, tex_folder, interactive)
+                    # add a new line after each file input
+                    if noline:
+                        pass
+                    else:
+                        output_lines.append('\n')
+                else:
+                    output_lines.append(line)
+            elif include_bbl and bbl_flag:
+                output_lines += bbl_file(base_file)
             else:
-                output_lines.append('\n')  # add a new line after each file input
-        elif include_bbl and line.startswith("\\bibliography") and (not line.startswith("\\bibliographystyle")):
-            output_lines += bbl_file(base_file)
-        else:
-            output_lines.append(line)
-    f.close()
+                output_lines.append(line)
     return output_lines
 
 
@@ -69,19 +101,33 @@ def bbl_file(base_file):
 
 
 @click.command()
-@click.argument('base_file', type = click.Path())
-@click.argument('output_file', type = click.Path())
+@click.argument('base_file', type=click.Path())
+@click.argument('output_file', type=click.Path())
 @click.option('--include_bbl/--no_bbl', default=False)
-@click.option("--noline", is_flag = True)
-def main(base_file, output_file, include_bbl = False, noline = False):
-
+@click.option('--noline', is_flag=True)
+@click.option('--tex_folder', default='')
+@click.option('--interactive', is_flag=True, default=False)
+def main(
+    base_file, output_file, include_bbl=False,
+    noline=False, tex_folder='', interactive=False):
     """
-    This "flattens" a LaTeX document by replacing all \input{X} lines w/ the
+    This "flattens" a LaTeX document by replacing all \\input{X} lines w/ the
     text actually contained in X. See associated README.md for details.
+
+    If .tex files are placed in a specific folder via input@path command in
+    the preamble of the latex file the tex_folder option must be specified.
+
+    Input:
+    base_file:      (str)   main .tex file to explore
+    output_file:    (str)   .tex file which will be produced as output
+    include_bbl:    (bool)  if True the bibliography is included
+    noline:         (bool)  avoid newline after merging files
+    tex_folder:     (str)   use specific .tex folder
     """
     current_path = os.path.split(base_file)[0]
-    g = open(output_file, "w")
-    g.write(''.join(expand_file(base_file, current_path, include_bbl, noline)))
-    g.close()
+    with open(output_file, "w") as file_to_write:
+        file_to_write.write(''.join(
+            expand_file(
+                base_file, current_path, include_bbl,
+                noline, tex_folder, interactive)))
     return None
-