Add cleaner paths (#43)

* ignore venv

* ignore pylians if unavaible

* Edit loading paths

* Edit paths

* Stop having default paths

* Add nb

* Add glamdring paths

---------

Co-authored-by: Richard Stiskalek <dc-stis1@login8b.pri.cosma7.alces.network>
Co-authored-by: Richard Stiskalek <dc-stis1@login8a.pri.cosma7.alces.network>

csiborgtools/__init__.py

@@ -13,3 +13,10 @@
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 from csiborgtools import (read, match, utils, units, fits, field, clustering)  # noqa
+
+# Arguments to csiborgtools.read.CSiBORGPaths.
+paths_glamdring = {
+    "srcdir": "/mnt/extraspace/hdesmond/",
+    "dumpdir": "/mnt/extraspace/rstiskalek/csiborg/",
+    "mmain_path": "/mnt/zfsusers/hdesmond/Mmain",
+    "initmatch_path": "/mnt/extraspace/rstiskalek/csiborg/initmatch/"}

csiborgtools/field/__init__.py

@@ -12,4 +12,9 @@
 # You should have received a copy of the GNU General Public License along
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-from .density import DensityField  # noqa
+from warnings import warn
+try:
+    import MAS_library as MASL
+    from .density import DensityField
+except ImportError:
+    warn("MAS_library not found, `DensityField` will not be available", UserWarning)  # noqa

csiborgtools/read/halo_cat.py

@@ -99,9 +99,7 @@ class HaloCatalogue:
         Loads the data, merges with mmain, does various coordinate transforms.
         """
         # Load the processed data
-        fname = "ramses_out_{}_{}.npy".format(
-            str(self.nsim).zfill(5), str(self.nsnap).zfill(5))
-        data = numpy.load(join(self.paths.dumpdir, fname))
+        data = numpy.load(self.paths.hcat_path(self.nsim))
 
         # Load the mmain file and add it to the data
         mmain = read_mmain(self.nsim, self.paths.mmain_path)

csiborgtools/read/readsim.py

@@ -35,13 +35,13 @@ class CSiBORGPaths:
 
     Parameters
     ----------
-    srcdir : str, optional
+    srcdir : str
         Path to the folder where CSiBORG simulations are stored.
-    dumpdir : str, optional
+    dumpdir : str
         Path to the folder where files from `run_fit_halos` are stored.
-    mmain_path : str, optional
+    mmain_path : str
         Path to folder where mmain files are stored.
-    initmatch_path : str, optional
+    initmatch_path : str
         Path to the folder where particle ID match between the first and final
         snapshot is stored.
     """
@@ -50,16 +50,12 @@ class CSiBORGPaths:
     _mmain_path = None
     _initmatch_path = None
 
-    def __init__(self, srcdir="/mnt/extraspace/hdesmond/",
-                 dumpdir="/mnt/extraspace/rstiskalek/csiborg/",
-                 mmain_path="/mnt/zfsusers/hdesmond/Mmain",
-                 initmatch_path="/mnt/extraspace/rstiskalek/csiborg/initmatch/"):  # noqa
-        for path in [srcdir, dumpdir, mmain_path, initmatch_path]:
-            self._check_directory(path)
-        self._srcdir = srcdir
-        self._dumpdir = dumpdir
-        self._mmain_path = mmain_path
-        self._initmatch_path = initmatch_path
+    def __init__(self, srcdir=None, dumpdir=None, mmain_path=None,
+                 initmatch_path=None):
+        self.srcdir = srcdir
+        self.dumpdir = dumpdir
+        self.mmain_path = mmain_path
+        self.initmatch_path = initmatch_path
 
     @staticmethod
     def _check_directory(path):
@@ -75,8 +71,17 @@ class CSiBORGPaths:
         -------
         path : str
         """
+        if self._srcdir is None:
+            raise ValueError("`srcdir` is not set!")
         return self._srcdir
 
+    @srcdir.setter
+    def srcdir(self, path):
+        if path is None:
+            return
+        self._check_directory(path)
+        self._srcdir = path
+
     @property
     def dumpdir(self):
         """
@@ -86,8 +91,17 @@ class CSiBORGPaths:
         -------
         path : str
         """
+        if self._dumpdir is None:
+            raise ValueError("`dumpdir` is not set!")
         return self._dumpdir
 
+    @dumpdir.setter
+    def dumpdir(self, path):
+        if path is None:
+            return
+        self._check_directory(path)
+        self._dumpdir = path
+
     @property
     def temp_dumpdir(self):
         """
@@ -111,8 +125,17 @@ class CSiBORGPaths:
         -------
         path : str
         """
+        if self._mmain_path is None:
+            raise ValueError("`mmain_path` is not set!")
         return self._mmain_path
 
+    @mmain_path.setter
+    def mmain_path(self, path):
+        if path is None:
+            return
+        self._check_directory(path)
+        self._mmain_path = path
+
     @property
     def initmatch_path(self):
         """
@@ -123,8 +146,17 @@ class CSiBORGPaths:
         -------
         path : str
         """
+        if self._initmatch_path is None:
+            raise ValueError("`initmatch_path` is not set!")
         return self._initmatch_path
 
+    @initmatch_path.setter
+    def initmatch_path(self, path):
+        if path is None:
+            return
+        self._check_directory(path)
+        self._initmatch_path = path
+
     def ic_ids(self, tonew):
         """
         CSiBORG IC realisation IDs from the list of folders in `self.srcdir`.
@@ -211,7 +243,7 @@ class CSiBORGPaths:
         cdir = join(self.dumpdir, "initmatch")
         return join(cdir, "clump_{}_{}.npy".format(nsim, "particles"))
 
-    def snapshot_path(self, nsnap, nsim, tonew=False):
+    def snapshot_path(self, nsnap, nsim):
         """
         Path to a CSiBORG IC realisation snapshot.
 
@@ -221,16 +253,33 @@ class CSiBORGPaths:
             Snapshot index.
         nsim : int
             IC realisation index.
-        tonew : bool, optional
-            Whether to return the path to the '_new' IC realisation.
 
         Returns
         -------
         snappath : str
         """
+        if nsnap == 1:
+            tonew = True
         simpath = self.ic_path(nsim, tonew=tonew)
         return join(simpath, "output_{}".format(str(nsnap).zfill(5)))
 
+    def hcat_path(self, nsim):
+        """
+        Path to the final snapshot halo catalogue from `fit_halos.py`.
+
+        Parameters
+        ----------
+        nsim : int
+            IC realisation index.
+
+        Returns
+        -------
+        path : str
+        """
+        nsnap = str(max(self.get_snapshots(nsim))).zfill(5)
+        fname = "ramses_out_{}_{}.npy".format(str(self.nsim).zfill(5), nsnap)
+        return join(self.dumpdir, fname)
+
 
 ###############################################################################
 #                          Fortran readers                                    #
@@ -248,7 +297,7 @@ class ParticleReader:
     _paths = None
 
     def __init__(self, paths):
-        assert isinstance(paths, CSiBORGPaths)
+#        assert isinstance(paths, CSiBORGPaths)
         self._paths = paths
 
     @property
@@ -306,7 +355,7 @@ class ParticleReader:
             Opened part files.
         """
         snappath = self.paths.snapshot_path(nsnap, nsim)
-        ncpu = int(self.read_info()["ncpu"])
+        ncpu = int(self.read_info(nsnap, nsim)["ncpu"])
         nsnap = str(nsnap).zfill(5)
         if verbose:
             print("Reading in output `{}` with ncpu = `{}`."