Add CI testing and fix a few minor module issues

docs/index.md

@@ -22,4 +22,4 @@ the advanced compute capabilities provided with the cluster.
 
 Students, faculty, or staff should register for the workshops in advance via the links below. Please bring your laptop to the workshop.
 
-<iframe src="https://libcal.smu.edu/widget/events/minicalendar?&cal_id=15527&l=50&tar=0&h=450&sp=0&audience=&c=8174-8175&z=" style="border-width:0" width="100%" height="464" frameborder="0" scrolling="no"></iframe>
+<iframe src="https://libcal.smu.edu/widget/events/minicalendar?&cal_id=15527&l=50&tar=0&h=450&sp=0&audience=&c=8174-8175&z=" style="border-width:0" width="100%" height="464" frameborder="0" scrolling="no"></iframe>

docs/portal.md

@@ -115,4 +115,3 @@ run modules and code with the Slurm scheduler from an SSH session.
     selecting the "Upload" button.
 -   You can download files and directories by selecting them and then
     selecting the "Download" button.
-

modules/m3/applications/crystal/23/1.0.1-1.lua

@@ -3,11 +3,10 @@ whatis("CRYSTAL 23 v1.0.1: Must be member of crystal group. Request access at vi
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject to join crystal group\n"
 
-local found = required_group("crystal")
-local found_new = required_group("hpc-crystal")
+local valid_groups = userInGroups("hpc-crystal")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("crystal")

modules/m3/applications/crystal/23/1.0.1.lua

@@ -3,11 +3,10 @@ whatis("CRYSTAL 23 v1.0.1: Must be member of crystal group. Request access at vi
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject to join crystal group\n"
 
-local found = required_group("crystal")
-local found_new = required_group("hpc-crystal")
+local valid_groups = userInGroups("hpc-crystal")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("crystal")

modules/m3/applications/gaussian/g09d.lua

@@ -3,11 +3,10 @@ whatis("Gaussian 09 D: Must be member of gaussian group. Request access at help@
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject to join gaussian group\n"
 
-local found = required_group("gaussian")
-local found_new = required_group("hpc-gaussian")
+local valid_groups = userInGroups("hpc-gaussian")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("gaussian")

modules/m3/applications/gaussian/g16c/haswell.lua

@@ -3,11 +3,10 @@ whatis("Gaussian 16 C.02: Must be member of gaussian group. Request access at he
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject to join gaussian group\n"
 
-local found = required_group("gaussian")
-local found_new = required_group("hpc-gaussian")
+local valid_groups = userInGroups("hpc-gaussian")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("gaussian")

modules/m3/applications/gaussian/g16c/zen3.lua

@@ -3,11 +3,10 @@ whatis("Gaussian 16 C.02: Must be member of gaussian group. Request access at he
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject to join gaussian group\n"
 
-local found = required_group("gaussian")
-local found_new = required_group("hpc-gaussian")
+local valid_groups = userInGroups("hpc-gaussian")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("gaussian")

modules/m3/applications/gaussview/6.0.16.lua

@@ -2,11 +2,10 @@ whatis("GaussView")
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject to join gaussian group\n"
 
-local found = required_group("gaussian")
-local found_new = required_group("hpc-gaussian")
+local valid_groups = userInGroups("hpc-gaussian")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("gaussview")

modules/m3/applications/vasp/5.4.4.lua

@@ -3,11 +3,10 @@ whatis("VASP 5.4.4: Must be member of vasp group. Request access at via help@smu
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject to join vasp group\n"
 
-local found = required_group("vasp")
-local found_new = required_group("hpc-vasp")
+local valid_groups = userInGroups("hpc-vasp")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("vasp")

modules/mp/apps/gaussian/g16c02.lua

@@ -3,11 +3,10 @@ whatis("Gaussian 16 C.02: Must be member of gaussian group. Request access at he
 local err_message="To use this module you must be in a particular group\n" ..
                   "Please contact help@smu.edu with HPC in the subject  to join gaussian group\n"
 
-local found = required_group("gaussian")
-local found_new = required_group("hpc-gaussian")
+local valid_groups = userInGroups("hpc-gaussian")
 
-if (not found and not found_new) then
-  LmodError(err_message)
+if (not valid_groups) then
+  LmodBreak(err_message)
 end
 
 family("gaussian")

modules/testing/biostats_r/1.0.0.lua

@@ -12,6 +12,7 @@ R -- launches an R terminal
 Rscript script -- run a script
 
 ]])
+
 whatis("Name: Biostats R")
 whatis("Version: ml-verse:4.4.1")
 whatis("Category: R")
@@ -21,7 +22,6 @@ family("R")
 
 extensions("DEMORT, stacks/2.68, freebayes, trimmonatic/0.39, bwa/0.7.18, pear/0.9.11, fastp/0.24.0, dDocent/2.9.8, fastx-toolkit, fastqc, bowtie2, htseq, star/2.7.11b, sra-tools/3.2.0")
 
-
 always_load('apptainer')
 local sif_file = '/hpc/m3/containers/biostats_r/biostats_r_1.0.0.sif'