diff --git a/bfps/FluidResize.py b/bfps/FluidResize.py
index 0cb0f561163ed3a7f080da5157562b90ab2c26dd..444c4d466fafd241a5f32127b2074cddb6b71a5a 100644
--- a/bfps/FluidResize.py
+++ b/bfps/FluidResize.py
@@ -142,15 +142,15 @@ class FluidResize(_fluid_particle_base):
cmd_line_pars[k] = opt.m
self.pars_from_namespace(opt)
src_file = os.path.join(
- opt.src_work_dir,
+ os.path.realpath(opt.src_work_dir),
opt.src_simname + '_cvorticity_i{0:0>5x}'.format(opt.src_iteration))
read_file = os.path.join(
self.work_dir,
opt.src_simname + '_cvorticity_i{0:0>5x}'.format(opt.src_iteration))
- if not os.path.exists(read_file):
- os.symlink(src_file, read_file)
self.set_host_info(bfps.host_info)
self.write_par(iter0 = opt.src_iteration)
+ if not os.path.exists(read_file):
+ os.symlink(src_file, read_file)
self.run(ncpu = opt.ncpu)
return None
diff --git a/bfps/NavierStokes.py b/bfps/NavierStokes.py
index 7ccc7ed2b6dbf8ca706c6e40a54ccfd10ae6462d..d263d432ab3138026fa4c58f434957635811c632 100644
--- a/bfps/NavierStokes.py
+++ b/bfps/NavierStokes.py
@@ -931,7 +931,7 @@ class NavierStokes(_fluid_particle_base):
'--src-wd',
type = str,
dest = 'src_work_dir',
- default = './')
+ default = '')
parser.add_argument(
'--src-simname',
type = str,
@@ -995,6 +995,8 @@ class NavierStokes(_fluid_particle_base):
self.parameters['max_Q_estimate'] = meantrS2
self.parameters['max_R_estimate'] = .4*meantrS2**1.5
+ if len(opt.src_work_dir) == 0:
+ opt.src_work_dir = opt.work_dir
self.pars_from_namespace(opt)
self.fill_up_fluid_code()
self.finalize_code()
@@ -1014,7 +1016,7 @@ class NavierStokes(_fluid_particle_base):
if not os.path.exists(init_condition_file):
if len(opt.src_simname) > 0:
src_file = os.path.join(
- self.work_dir,
+ os.path.realpath(opt.src_work_dir),
opt.src_simname + '_cvorticity_i{0:0>5x}'.format(opt.src_iteration))
os.symlink(src_file, init_condition_file)
else:
diff --git a/bfps/_base.py b/bfps/_base.py
index 78667424a6e455f20158e317f0e82868f5b21904..eb564fcd3669eea5f0d667cd4e94c88e06540ccf 100644
--- a/bfps/_base.py
+++ b/bfps/_base.py
@@ -45,7 +45,7 @@ class _base(object):
'ny' : 32,
'nz' : 32}
self.string_length = 512
- self.work_dir = work_dir
+ self.work_dir = os.path.realpath(work_dir)
self.simname = simname
return None
def cdef_pars(self):
diff --git a/documentation/_static/development.rst b/documentation/_static/development.rst
index d2aa9da37c0822aa82b635c7684b8f990146e079..446bc1ab765a281f05410939c74e8c08dabaf3e6 100644
--- a/documentation/_static/development.rst
+++ b/documentation/_static/development.rst
@@ -7,23 +7,23 @@ Development
Versioning guidelines
---------------------
-Version tracking for `bfps` is done with `git` (see https://git-scm.com/
+Version tracking for :mod:`bfps` is done with ``git`` (see https://git-scm.com/
for description).
The branching model described at
http://nvie.com/posts/a-successful-git-branching-model/ should be
adhered to as strictly as possible.
-The usable `VERSION` number will be constructed according to semantic
-versioning rules (see http://semver.org/), `MAJOR.MINOR.PATCH`.
-In principle, if you use `bfps` and you've created children of the
-`NavierStokes` class, you should not need to rewrite your code unless
-the `MAJOR` version changes.
+The usable ``VERSION`` number will be constructed according to semantic
+versioning rules (see http://semver.org/), ``MAJOR.MINOR.PATCH``.
+In principle, if you use :mod:`bfps` and you've created children of the
+:class:`NavierStokes <bfps.NavierStokes.NavierStokes>` class, you should not need to rewrite your code unless
+the ``MAJOR`` version changes.
-There are 2 main branches, `master` and `develop`.
-`setup.py` will call `git` to read in the `VERSION`: it will get the
+There are 2 main branches, ``master`` and ``develop``.
+``setup.py`` will call ``git`` to read in the ``VERSION``: it will get the
latest available tag.
-If the active branch name contains either of the strings `develop`,
-`feature` or `bugfix`, then the full output of `git describe --tags`
+If the active branch name contains either of the strings ``develop``,
+``feature`` or ``bugfix``, then the full output of ``git describe --tags``
will be used;
otherwise, only the string before the dash (if a dash exists) will be
used.
@@ -32,25 +32,28 @@ At the moment the following rules seem adequate.
Once I get feedback from someone who actually knows how to handle bigger
projects, these may change.
-1. New features are worked on in branches forked from `develop`, with
- the branch name of the form `feature/bla`.
- Feature branches are merged back into `develop` only after all tests
+1. New features are worked on in branches forked from ``develop``, with
+ the branch name of the form ``feature/bla``.
+ Feature branches are merged back into ``develop`` only after all tests
pass.
-2. Whenever the `develop` branch is merged into `master`, the last
- commit on the `develop` branch is tagged with `MAJOR.MINOR`.
-3. Whenever a bug is discovered in version X.Y, a new branch called `vX.Y`
- is forked from the corresponding `master` merge point.
- A new bugfix branch is forked from `vX.Y`, the bug is fixed, and then
- this bugfix branch is merged into all affected branches (this includes
- `vX.Y`).
- After merging, the respective merge points are tagged adequately (`vX.Y`
- gets the tag X.Y.1).
+2. Whenever the ``develop`` branch is merged into ``master``, the last
+ commit on the ``develop`` branch is tagged with ``MAJOR.MINOR``.
+3. Whenever a bug is discovered in version X.Y, a new branch called ``vX.Y``
+ is forked from the corresponding ``master`` merge point.
+ A new bugfix branch is forked from ``vX.Y``, the bug is fixed.
+ The last commit in the bugfix branch is tagged X.Y.1.
+ This bugfix branch is merged into all affected branches (this includes
+ ``vX.Y``).
+ After merging, the respective merge points into branches other than
+ ``develop``, ``bugfix`` or ``feature`` are tagged accordingly;
+ there's no need to tag ``develop`` etc since those contain the git
+ commit in the version anyway.
4. Whenever a bug is discovered in version X.Y.Z, a bugfix branch is
- forked from `vX.Y`, and then rule 3 is adapted accordingly.
+ forked from ``vX.Y``, and then rule 3 is adapted accordingly.
------------
Code testing
------------
-Testing for `bfps` is done with `tox`.
+Testing for :mod:`bfps` is done with ``tox``.