Updated commands to use limited integer ranges

Signed-off-by: Timothy Click <tcthepoet@yahoo.com>

src/fluctmatch/commands/cmd_convert.py

@@ -104,7 +104,7 @@
     "charmm_version",
     metavar="VERSION",
     default=41,
-    type=click.INT,
+    type=click.IntRange(27, None, clamp=True),
     help="CHARMM version",
 )
 @click.option(

src/fluctmatch/commands/cmd_diff.py

@@ -52,8 +52,8 @@
     "--ressep",
     metavar="RESSEP",
     default=3,
-    type=click.INT,
-    help="Separation between residues (I,I+n)"
+    type=click.IntRange(0, None, clamp=True),
+    help="Number of residues to exclude in I,I+r (default: 2)"
 )
 @click.argument(
     "table1",
@@ -105,7 +105,7 @@ def cli(outdir, ressep, table1, table2):
 
     filename = path.join(outdir, "dcoupling.txt")
     with open(filename, mode="wb") as output:
-        print("Writing table differences to {}".format(filename))
+        click.echo("Writing table differences to {}".format(filename))
         d_table = d_table.to_csv(
             header=True,
             index=True,
@@ -129,7 +129,7 @@ def cli(outdir, ressep, table1, table2):
 
     filename = path.join(outdir, "dinteractions.txt")
     with open(filename, mode="wb") as output:
-        print("Writing residue-residue differences to {}".format(filename))
+        click.echo("Writing residue-residue differences to {}".format(filename))
         d_interactions = d_interactions.to_csv(
             header=True,
             index=True,

src/fluctmatch/commands/cmd_framediff.py

@@ -52,8 +52,8 @@
     "--ressep",
     metavar="RESSEP",
     default=3,
-    type=click.INT,
-    help="Separation between residues (I,I+n)"
+    type=click.IntRange(0, None, clamp=True),
+    help="Number of residues to exclude in I,I+r (default: 2)"
 )
 @click.argument(
     "table",
@@ -85,7 +85,7 @@ def cli(outdir, ressep, table):
 
     filename = path.join(outdir, "dframe_coupling.txt")
     with open(filename, mode="wb") as output:
-        print("Writing frame differences to {}".format(filename))
+        click.echo("Writing frame differences to {}".format(filename))
         d_table = d_table.to_csv(
             header=True,
             index=True,
@@ -97,7 +97,7 @@ def cli(outdir, ressep, table):
 
     filename = path.join(outdir, "dframe_perres.txt")
     with open(filename, mode="wb") as output:
-        print("Writing per residue frame differences to {}".format(filename))
+        click.echo("Writing per residue frame differences to {}".format(filename))
         d_perres = d_perres.to_csv(
             header=True,
             index=True,
@@ -109,7 +109,7 @@ def cli(outdir, ressep, table):
 
     filename = path.join(outdir, "dframe_interactions.txt")
     with open(filename, mode="wb") as output:
-        print(
+        click.echo(
             "Writing residue-residue frame differences to {}".format(filename)
         )
         d_interactions = d_interactions.to_csv(

src/fluctmatch/commands/cmd_normdiff.py

@@ -53,8 +53,8 @@
     "--ressep",
     metavar="RESSEP",
     default=3,
-    type=click.INT,
-    help="Separation between residues (I,I+n)"
+    type=click.IntRange(0, None, clamp=True),
+    help="Number of residues to exclude in I,I+r (default: 2)"
 )
 @click.argument(
     "kb",

src/fluctmatch/commands/cmd_sca.py

@@ -73,16 +73,11 @@
 @click.option(
     "-r",
     "--ressep",
+    metavar="RESSEP",
     default=2,
     type=click.IntRange(0, None, clamp=True),
     help="Number of residues to exclude in I,I+r (default: 2)"
 )
-@click.option(
-    "-s",
-    "--subset",
-    type=(native_str, click.IntRange(1, None, clamp=True), click.IntRange(1, None, clamp=True)),
-    multiple=True, help="Subset of a system (SEGID FIRST LAST)"
-)
 @click.option(
     "-o",
     "--output",
@@ -103,7 +98,7 @@
     )
 )
 def calculate_scafluct(
-    ntrials, std, kpos, pcut, ressep, subset, output, filename
+    ntrials, std, kpos, pcut, ressep, output, filename
 ):
     # Load the table, separate by I,I+r, and if requested, create a subset.
     table = ParamTable(ressep=ressep)

src/fluctmatch/commands/cmd_splittraj.py

@@ -137,31 +137,31 @@
     "--system",
     metavar="NDXNUM",
     default=0,
-    type=click.INT,
+    type=click.IntRange(0, None, clamp=True),
     help="System selection based upon Gromacs index file",
 )
 @click.option(
     "-b",
     "start",
     metavar="FRAME",
     default=1,
-    type=click.INT,
+    type=click.IntRange(1, None, clamp=True),
     help="Start time of trajectory",
 )
 @click.option(
     "-e",
     "stop",
     metavar="FRAME",
     default=10000,
-    type=click.INT,
+    type=click.IntRange(1, None, clamp=True),
     help="Stop time of total trajectory",
 )
 @click.option(
     "-w",
     "window_size",
     metavar="WINSIZE",
     default=10000,
-    type=click.INT,
+    type=click.IntRange(2, None, clamp=True),
     help="Size of each subtrajectory",
 )
 def cli(

src/fluctmatch/commands/cmd_stats.py

@@ -65,8 +65,8 @@
     "--ressep",
     metavar="RESSEP",
     default=3,
-    type=click.INT,
-    help="Separation between residues (I,I+n)"
+    type=click.IntRange(0, None, clamp=True),
+    help="Number of residues to exclude in I,I+r (default: 2)"
 )
 @click.option(
     "-t",
@@ -97,7 +97,7 @@ def cli(stats, hist, outdir, ressep, tbltype, table):
             "_".join((tbltype.lower(), "table", "stats.txt"))
         )
         with open(filename, mode="wb") as stat_file:
-            print("Writing table statistics to {}".format(filename))
+            click.echo("Writing table statistics to {}".format(filename))
             info = ps.table_stats().to_csv(
                 header=True,
                 index=True,
@@ -110,7 +110,7 @@ def cli(stats, hist, outdir, ressep, tbltype, table):
         if tbltype == "Kb":
             filename = path.join(outdir, "interaction_stats.txt")
             with open(filename, mode="wb") as stat_file:
-                print(
+                click.echo(
                     "Writing residue-residue statistics to {}".format(filename)
                 )
                 ps._table._ressep = 0
@@ -125,7 +125,7 @@ def cli(stats, hist, outdir, ressep, tbltype, table):
 
             filename = path.join(outdir, "residue_stats.txt")
             with open(filename, mode="wb") as stat_file:
-                print(
+                click.echo(
                     "Writing individual residue statistics "
                     "to {}".format(filename)
                 )
@@ -145,7 +145,7 @@ def cli(stats, hist, outdir, ressep, tbltype, table):
             "_".join((tbltype.lower(), "table", "hist.txt"))
         )
         with open(filename, mode="wb") as stat_file:
-            print("Writing table histogram to {}".format(filename))
+            click.echo("Writing table histogram to {}".format(filename))
             info = ps.table_hist().to_csv(
                 index=True,
                 sep=native_str(" "),
@@ -157,7 +157,7 @@ def cli(stats, hist, outdir, ressep, tbltype, table):
         if tbltype == "Kb":
             filename = path.join(outdir, "interaction_hist.txt")
             with open(filename, mode="wb") as stat_file:
-                print(
+                click.echo(
                     "Writing residue-residue histogram to {}".format(filename)
                 )
                 ps._table._ressep = 0
@@ -171,7 +171,7 @@ def cli(stats, hist, outdir, ressep, tbltype, table):
 
             filename = path.join(outdir, "residue_hist.txt")
             with open(filename, mode="wb") as stat_file:
-                print(
+                click.echo(
                     "Writing individual residue histogram "
                     "to {}".format(filename)
                 )

src/fluctmatch/commands/cmd_table.py

@@ -80,8 +80,8 @@
     "--ressep",
     metavar="RESSEP",
     default=3,
-    type=click.INT,
-    help="Separation between residues (I,I+n)"
+    type=click.IntRange(0, None, clamp=True),
+    help="Number of residues to exclude in I,I+r (default: 2)"
 )
 @click.option(
     "-v",

src/fluctmatch/commands/cmd_thermo.py

@@ -106,7 +106,7 @@
     "charmm_version",
     metavar="VERSION",
     default=41,
-    type=click.INT,
+    type=click.IntRange(27, None, clamp=True),
     help="CHARMM version",
 )
 def cli(

src/fluctmatch/commands/cmd_wordom.py

@@ -66,22 +66,22 @@
     "start",
     metavar="FRAME",
     default=0,
-    type=click.INT,
+    type=click.IntRange(0, None, clamp=True),
     help="Start time of trajectory",
 )
 @click.option(
     "-e",
     "stop",
     metavar="FRAME",
-    type=click.INT,
+    type=click.IntRange(0, None, clamp=True),
     help="Stop time of total trajectory",
 )
 @click.option(
     "-dt",
     "step",
     metavar="STEP",
     default=1,
-    type=click.INT,
+    type=click.IntRange(1, None, clamp=True),
     help="Interval between frames"
 )
 @click.option(

src/fluctmatch/commands/cmd_write_charmm.py

@@ -74,7 +74,7 @@
     "charmm_version",
     metavar="VERSION",
     default=41,
-    type=click.INT,
+    type=click.IntRange(27, None, clamp=True),
     help="CHARMM version",
 )
 @click.option(