Merge pull request #271 from ksahlin/contributing

Get started on documenting how to contribute

.clang-format

@@ -0,0 +1,13 @@
+---
+Language:        Cpp
+BasedOnStyle:  Chromium
+AlignAfterOpenBracket: BlockIndent
+IndentWidth:     4
+ColumnLimit:     110
+ReflowComments:  false
+BreakConstructorInitializers: BeforeComma
+BreakInheritanceList: BeforeComma
+SpaceAfterCStyleCast: true
+SpaceInEmptyBlock: true
+
+# Possibly configure IncludeCategories

CONTRIBUTING.md

@@ -0,0 +1,56 @@
+# Contributing
+
+Contributions to strobealign are very welcome!
+
+- To report a bug,
+  [open an issue](https://github.com/ksahlin/strobealign/issues/new).
+- To suggest a small change, just submit a pull request.
+- To suggest a larger change, it may be a good idea to first open an issue or
+  to send an e-mail so we can discuss it.
+
+Instead of one large PR, consider submitting multiple small, logically
+self-contained PRs if it makes sense. This facilitates review and allows for a
+more focused discussion.
+
+## Debugging
+
+When compiling strobealign, you can add `-DCMAKE_BUILD_TYPE=RelWithDebInfo` to
+the `cmake` options to get debug symbols.
+
+If needed, run `make` with `VERBOSE=1` to get more logging output.
+
+## Testing
+
+After CMake has been run, you can use this one-liner to compile strobealign and
+run the tests:
+```
+make -j -C build && tests/run.sh
+```
+
+Whenever you make changes that could potentially affect mapping results, you can
+run a more elaborate test that compares strobealign against a “baseline”
+(know good) commit. Just run this script:
+```
+tests/compare-baseline.sh
+```
+The first time, it will download a *D. melanogaster* genome and some reads from
+the Sequence Read Archive (SRA). Since the dataset is truncated to the first
+100'000 reads, mapping it should take less than 30 seconds.
+
+The baseline commit is configured in `tests/baseline-commit.txt`. The script
+builds strobealign from that commit and runs it against the downloaded test
+data, then builds strobealign as it is in your working copy and compares the
+two produced BAM files. The baseline BAM is cached and re-used as long as the
+baseline commit does not change.
+
+
+## Style guide
+
+Existing code in strobealign is currently not necessarily consistent with this
+style guide, but new code should follow it.
+
+* Use the `clang-format` code formatter with the `-style=file` option.
+* Use Python-like naming of functions, methods, variables, etc. That is, it
+  should be `ClassName`, `variable_name`, `method_name`, `CONSTANT`.
+* The header guard of a file named `xyz.hpp` should be named
+  `STROBEALIGN_XYZ_HPP`.

README.md

@@ -192,40 +192,7 @@ See [Changelog](CHANGES.md).
 Contributing
 ------------
 
-Contributions to strobealign are very welcome! For small things, just submit a
-PR. When you want to make larger changes, it may be a good idea to first open an
-issue or to send an e-mail so we can discuss it.
-
-## Compiling
-
-When compiling strobealign, you can add `-DCMAKE_BUILD_TYPE=RelWithDebInfo` to
-the `cmake` options to get debug symbols.
-
-If needed, run `make` with `VERBOSE=1` to get more logging output.
-
-After CMake has been run, you can use this one-liner to compile strobealign and
-run the tests:
-```
-make -j -C build && tests/run.sh
-```
-
-## Testing
-
-Whenever you make changes that could potentially affect mapping results, you can
-run a more elaborate test that compares strobealign against a “baseline”
-(know good) commit. Just run this script:
-```
-tests/compare-baseline.sh
-```
-The first time, it will download the D. melanogaster genome and some reads from
-the SRA. Since the dataset is truncated to the first 100'000 reads, mapping it
-should take less than 30 seconds.
-
-The baseline commit is configured in `tests/baseline-commit.txt`. The script
-builds strobealign from that commit and runs it against the downloaded test
-data, then builds strobealign as it is in your working copy and compares the
-two produced BAM files. The baseline BAM is cached and re-used as long as the
-baseline commit does not change.
+See [Contributing](CONTRIBUTING.md).
 
 
 V0.7 Performance