updated and cleaned up readme

2 files changed, 16 insertions, 17 deletions

diff --git a/README.md b/README.md
index 445d8eb..36b041c 100644
--- a/README.md
+++ b/README.md
@@ -24,22 +24,22 @@ Input formats currently supported by Ripser:
   - comma-separated values upper triangular distance matrix (MATLAB output from the function `pdist`)
   - comma-separated values full distance matrix
   - [DIPHA] distance matrix data
-  - sparse distance matrix in Sparse Triplet format
+  - sparse distance matrix in sparse triplet format
   - binary lower triangular distance matrix
   - point cloud data
 
-Ripser's efficiency is based on a few important concepts and principles, building on key previous and concurrent  developments by other researchers in computational topology:
+Ripser's efficiency is based on a few important concepts and principles, building on key previous and concurrent developments by other researchers in computational topology:
   
   - Compute persistent *co*homology (as suggested by [Vin de Silva, Dmitriy Morozov, and Mikael Vejdemo-Johansson](https://doi.org/10.1088/0266-5611/27/12/124003))
-  - Don't compute information that is never needed
-    (for the experts: employ the *clearing* optimization, aka *persistence with a twist*, as suggested by [Chao Chen and Michael Kerber](http://www.geometrie.tugraz.at/kerber/kerber_papers/ck-phcwat-11.pdf))
-  - Don't store information that can be readily recomputed (in particular, the boundary matrix and the reduced boundary matrix)
-  - Take computational shortcuts (*apparent* and *emergent persistence pairs*)
+  - Use the chain complex property that boundaries are cycles
+    (employ the *clearing* optimization, aka *persistence with a twist*, as suggested by [Chao Chen and Michael Kerber](http://www.geometrie.tugraz.at/kerber/kerber_papers/ck-phcwat-11.pdf))
   - If no threshold is specified, choose the *enclosing radius* as the threshold, from which on homology is guaranteed to be trivial (as suggested by [Greg Henselman-Petrusek](https://github.com/Eetion/Eirene.jl))
+  - Don't store information that can be readily recomputed (in particular, the original and the reduced boundary matrix)
+  - Take computational shortcuts (*apparent* and *emergent persistence pairs*)
 
 
 ### Version
-[Latest release][latest-release]: 1.1 (July 2019)
+[Latest release][latest-release]: 1.1 (August 2019)
 
 
 ### Building
@@ -58,6 +58,7 @@ make
 
 Ripser supports several compile-time options. They are switched on by defining the C preprocessor macros listed below, either using `#define` in the code or by passing an argument to the compiler. The following options are supported:
 
+  - `USE_COEFFICIENTS`: enable support for coefficients in a prime field
   - `INDICATE_PROGRESS`: indicate the current progress in the console
   - `PRINT_PERSISTENCE_PAIRS`: output the computed persistence pairs (enabled by default in the code; comment out to disable)
   - `USE_GOOGLE_HASHMAP`: enable support for Google's [sparsehash] data structure; may further reduce memory footprint
@@ -77,12 +78,12 @@ The input is given either in a file whose name is passed as an argument, or thro
     - `upper-distance`: upper triangular distance matrix; similar to the previous, but for the entries above the diagonal; suitable for output from the MATLAB functions `pdist` or  `seqpdist`, exported to a CSV file.
     - `distance`: full distance matrix; similar to the above, but for all entries of the distance matrix. One line per row of the matrix; only the part below the diagonal is actually read.
     - `dipha`: DIPHA distance matrix as described on the [DIPHA] website.
-    - `point-cloud`: point cloud; a comma (or whitespace, or other non-numerical character)  separated list of coordinates of the points in some Euclidean space, one point per line.
-    - `sparse`: sparse distance matrix in Sparse Triplet format
+    - `point-cloud`: point cloud; a comma (or whitespace, or other non-numerical character) separated list of coordinates of the points in some Euclidean space, one point per line.
     - `binary`: lower distance matrix in binary file format; a sequence of the distance matrix entries below the diagonal in 64 bit double format (IEEE 754, little endian).
+    - `sparse`: sparse triplet format; a whitespace separated list of entries of a sparse distance matrix, one entry per line, each of the form *i j d(i,j)* specifying the distance between points *i* and *j*.  Each pair of points should appear in the file at most once.
   - `--dim k`: compute persistent homology up to dimension *k*.
   - `--threshold t`: compute Rips complexes up to diameter *t*.
-  - `--modulus p`: compute homology with coefficients in the prime field Z/*p*Z.
+  - `--modulus p`: compute homology with coefficients in the prime field Z/*p*Z (only available when built with the option `USE_COEFFICIENTS`).
   - `--ratio <r>`: only show persistence pairs with death/birth ratio > *r*.
 
 
@@ -95,12 +96,10 @@ The following experimental features are currently available in separate branches
 - `representative-cycles`: computation and output of representative cycles for persistent homology (in the standard version, only *co*cycles are computed).
 - `simple`: a simplified version of Ripser, without support for sparse distance matrices and coefficients.  This might be a good starting point for exploring the code.
 
-Prototype implementations are already avaliable; please contact the author if one of these features might be relevant for your research.
-
 
 ### License
 
-Ripser is licensed under the [MIT] license (`COPYING.txt`), with an extra clause (`CONTRIBUTING.txt`) clarifying the license for modifications released without an explicit written license agreement. Please contact the author if you want to use Ripser in your software under a different license. 
+Ripser is licensed under the [MIT] license (`COPYING.txt`), with an extra clause (`CONTRIBUTING.txt`) clarifying the license for modifications released without an explicit written license agreement.  Please contact the author if you want to use Ripser in your software under a different license. 
 
 [Ulrich Bauer]: <http://ulrich-bauer.org>
 [live.ripser.org]: <http://live.ripser.org>
diff --git a/ripser.cpp b/ripser.cpp
index 8fb0cd1..c1d4fb3 100644
--- a/ripser.cpp
+++ b/ripser.cpp
@@ -998,17 +998,17 @@ void print_usage_and_exit(int exit_code) {
 	    << "                     distance       (full distance matrix)" << std::endl
 	    << "                     point-cloud    (point cloud in Euclidean space)" << std::endl
 	    << "                     dipha          (distance matrix in DIPHA file format)" << std::endl
-	    << "                     sparse         (sparse distance matrix in Sparse Triplet format)"
+	    << "                     sparse         (sparse distance matrix in sparse triplet format)"
 	    << std::endl
 	    << "                     binary         (lower triangular distance matrix in binary format)"
 	    << std::endl
 	    << "  --dim <k>        compute persistent homology up to dimension k" << std::endl
 	    << "  --threshold <t>  compute Rips complexes up to diameter t" << std::endl
 #ifdef USE_COEFFICIENTS
-	    << "  --modulus <p>    compute homology with coefficients in the prime field Z/pZ"
+	    << "  --modulus <p>    compute homology with coefficients in the prime field Z/pZ" << std::endl
 #endif
-	    << std::endl
-	    << "  --ratio <r>      only show persistence pairs with death/birth ratio > r" << std::endl;
+	    << "  --ratio <r>      only show persistence pairs with death/birth ratio > r" << std::endl
+	    << std::endl;
 	exit(exit_code);
 }