Merge branch 'bugfix/src-linking' into v1.0

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
 

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:

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):

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``.