Changed the binary path

Dockerfile

@@ -1,8 +1,8 @@
 FROM python:3.10-slim-bookworm AS build
 
-RUN mkdir -p /binaries/
+RUN mkdir -p /calcus/binaries/
 COPY scripts /calcus/scripts
-COPY bin /binaries/xtb
+COPY bin /calcus/binaries/xtb
 RUN python /calcus/scripts/extract_xtb.py
 
 RUN apt update && apt install build-essential gcc libxm4 libgl1 libmagic1 -y
@@ -16,7 +16,7 @@ RUN pip install -r /calcus/requirements.txt
 
 FROM python:3.10-slim-bookworm AS calcus_user
 
-COPY --from=0 /binaries/ /binaries/
+COPY --from=0 /calcus/binaries/ /calcus/binaries/
 
 ARG CALCUS_VERSION_HASH
 ENV CALCUS_VERSION_HASH=${CALCUS_VERSION_HASH}
@@ -26,14 +26,14 @@ ENV CALCUS_KEY_HOME "/calcus/keys"
 ENV CALCUS_TEST_SCR_HOME "/calcus/scratch/scr"
 ENV CALCUS_TEST_KEY_HOME "/calcus/scratch/keys"
 
-ENV EBROOTORCA "/binaries/orca"
-ENV GAUSS_EXEDIR "/binaries/g16"
-ENV XTB4STDAHOME "/binaries/xtb"
-ENV XTBPATH "/binaries/xtb/xtb:$XTB4STDAHOME"
-ENV STDAHOME "/binaries/xtb"
+ENV EBROOTORCA "/calcus/binaries/orca"
+ENV GAUSS_EXEDIR "/calcus/binaries/g16"
+ENV XTB4STDAHOME "/calcus/binaries/xtb"
+ENV XTBPATH "/calcus/binaries/xtb/xtb:$XTB4STDAHOME"
+ENV STDAHOME "/calcus/binaries/xtb"
 
 ENV PATH=$PATH:$XTB4STDAHOME/xtb/bin:$XTB4STDAHOME:$EBROOTORCA:$GAUSS_EXEDIR
-ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/binaries/orca:/usr/lib/openmpi/
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/calcus/binaries/orca:/usr/lib/openmpi/
 
 ENV PYTHONUNBUFFERED 1
 

cloud-compose.yml

@@ -1,5 +1,3 @@
-version: "3.4"
-
 services:  
         redis:
                 image: redis:latest

dev-compose.yml

@@ -1,5 +1,3 @@
-version: "3.4"
-
 services:  
         redis:
                 image: redis:latest

docker-compose.yml

@@ -1,5 +1,3 @@
-version: "3.4"
-
 services:  
         redis:
                 image: redis:latest

docker/slurm/Dockerfile

@@ -11,11 +11,11 @@ RUN yes "clustertest" | passwd slurm
 
 ENV EBROOTORCA "/home/slurm/orca"
 ENV GAUSS_EXEDIR "/home/slurm/g16"
-ENV XTB4STDAHOME "/binaries/xtb/"
+ENV XTB4STDAHOME "/calcus/binaries/xtb/"
 ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/home/slurm/orca"
 
 ENV PATH=$PATH:"/home/slurm/xtb:/home/slurm/g16:/home/slurm/orca:/home/slurm/other:/home/slurm/openmpi"
-ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/binaries/orca:/usr/lib/openmpi/
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/calcus/binaries/orca:/usr/lib/openmpi/
 
 ADD slurm.conf /etc/slurm-llnl/
 ADD cgroup.conf /etc/slurm-llnl/

frontend/calculation_unittest.py

@@ -7,8 +7,8 @@
 from django.core.management import call_command
 
 from frontend import tasks
-from .libxyz import *
-from .models import *
+from .libxyz import get_angle, parse_xyz_from_text
+from .models import np
 from .gen_calc import gen_calc
 from .tasks import run_calc
 from .calcusliveserver import SCR_DIR

frontend/calcusliveserver.py

@@ -39,10 +39,18 @@
 
 from django.contrib.staticfiles.testing import StaticLiveServerTestCase
 from django.core.management import call_command
-from django.contrib.auth.models import User
 
-from .models import *
-from .environment_variables import *
+from .models import (
+    Calculation,
+    CalculationOrder,
+    Ensemble,
+    Molecule,
+    Project,
+    ResearchGroup,
+    settings,
+    User,
+)
+from .environment_variables import CALCUS_KEY_HOME, CALCUS_SCR_HOME
 
 tests_dir = os.path.join("/".join(__file__.split("/")[:-1]), "tests/")
 dir_path = os.path.dirname(os.path.realpath(__file__))
@@ -1773,7 +1781,7 @@ def get_name_presets(self):
 
     def select_preset(self, name):
         self.wait_for_ajax()
-        element = WebDriverWait(self.driver, 2).until(
+        WebDriverWait(self.driver, 2).until(
             EC.presence_of_element_located(
                 (By.XPATH, f"//*[@id='presets']/option[text()='{name}']")
             )
@@ -2173,7 +2181,7 @@ def subscribe(self, plan, email, card_number, length="month"):
         if length == "year":
             switch = WebDriverWait(self.driver, 5).until(
                 EC.presence_of_element_located(
-                    (By.CSS_SELECTOR, f"[for=sub_length_switch]")
+                    (By.CSS_SELECTOR, "[for=sub_length_switch]")
                 )
             )
             switch.click()

frontend/cloud_job.py

@@ -4,7 +4,7 @@
 
 from django.conf import settings
 
-from .environment_variables import *
+from .environment_variables import IS_TEST
 from .helpers import job_triage
 
 if settings.IS_CLOUD:

frontend/cluster_daemon.py

@@ -79,8 +79,8 @@ class ConnectionCodes:
 os.environ.setdefault("DJANGO_SETTINGS_MODULE", "calcus.settings")
 django.setup()
 
-from frontend.models import *
-from frontend.environment_variables import *
+from frontend.models import Calculation, ClusterAccess, ErrorCodes
+from frontend.environment_variables import CALCUS_KEY_HOME, CALCUS_SCR_HOME
 from frontend import tasks
 
 

frontend/context.py

@@ -29,6 +29,6 @@ def default(request):
         try:
             d["SUBSCRIPTION_DATA"] = constants.SUBSCRIPTION_DATA[version]
         except (NameError, AttributeError):
-            logger.error(f"Could not get subscription data")
+            logger.error("Could not get subscription data")
 
     return d

frontend/decorators.py

@@ -17,7 +17,7 @@
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 
-from django.http import HttpResponse, HttpResponseRedirect
+from django.http import HttpResponseRedirect
 
 
 def superuser_required(func):

frontend/environment_variables.py

@@ -57,4 +57,4 @@
 
 MEM = int(PAL) * STACKSIZE
 EBROOTORCA = os.environ.get("EBROOTORCA", "")
-MULTIWFN_DIR = os.environ.get("MULTIWFN_DIR", "/binaries/xtb/")
+MULTIWFN_DIR = os.environ.get("MULTIWFN_DIR", "/calcus/binaries/xtb/")

frontend/forms.py

@@ -71,13 +71,13 @@ def save(self, commit=True):
 
         if commit:
             user.save()
-            r = ResourceAllocation.objects.create(
+            ResourceAllocation.objects.create(
                 code=get_random_string(),
                 redeemer=user,
                 allocation_seconds=settings.FREE_DEFAULT_COMP_SECONDS,
                 note=ResourceAllocation.NEW_ACCOUNT,
             )
-            proj = Project.objects.create(name="My Main Project", author=user)
+            Project.objects.create(name="My Main Project", author=user)
 
         return user
 
@@ -119,17 +119,17 @@ def validate_access_code(self):
         classes = ClassGroup.objects.filter(access_code=code)
 
         if classes.count() == 0:
-            raise ValidationError(f"No group found with such access code")
+            raise ValidationError("No group found with such access code")
         elif classes.count() > 1:
             logger.error(f"Multiple groups found with access code {code}!")
-            raise ValidationError(f"Internal error")
+            raise ValidationError("Internal error")
         elif classes.count() == 1:
             self.student_class = classes.first()
         else:
             logger.error(
                 f"Unexpected number of groups found with access code {code}: {classes.count()}!"
             )
-            raise ValidationError(f"Internal error")
+            raise ValidationError("Internal error")
 
     def save(self, commit=True):
         user = super().save(commit=False)
@@ -188,13 +188,13 @@ def save(self, commit=True):
 
         if commit:
             user.save()
-            r = ResourceAllocation.objects.create(
+            ResourceAllocation.objects.create(
                 code=get_random_string(),
                 redeemer=user,
                 allocation_seconds=settings.TRIAL_DEFAULT_COMP_SECONDS,
                 note=ResourceAllocation.TRIAL,
             )
-            proj = Project.objects.create(name="My Main Project", author=user)
+            Project.objects.create(name="My Main Project", author=user)
 
         return user
 
@@ -239,7 +239,7 @@ def save(self, commit=True):
 
         if commit:
             user.save()
-            r = ResourceAllocation.objects.create(
+            ResourceAllocation.objects.create(
                 code=get_random_string(),
                 redeemer=user,
                 allocation_seconds=(

frontend/gen_calc.py

@@ -17,7 +17,17 @@
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 
-from .models import *
+from .models import (
+    BasicStep,
+    Calculation,
+    CalculationOrder,
+    Ensemble,
+    Molecule,
+    Parameters,
+    Project,
+    Structure,
+    os,
+)
 from .tasks import generate_xyz_structure
 
 TESTS_DIR = os.path.join("/".join(__file__.split("/")[:-1]), "tests/")

frontend/gen_data_documentation.py

@@ -17,7 +17,7 @@
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 
-from constants import *
+from .constants import SOFTWARE_BASIS_SETS, SOFTWARE_METHODS
 
 TABLE_TEMPLATE = """
 <table class="table">

frontend/helpers.py

@@ -23,7 +23,7 @@
 from django.conf import settings
 from xkcdpass import xkcd_password as xp
 
-from .constants import *
+from .constants import ATOMIC_NUMBER, ATOMIC_SYMBOL, BOHR_VAL
 
 full_alphabet = string.ascii_letters + string.digits
 

frontend/libxyz.py

@@ -18,12 +18,16 @@
 """
 
 import json
-import numpy as np
 import periodictable
 import copy
-from .constants import *
-
 from hashlib import md5
+import numpy as np
+from numpy.linalg import expm, norm
+from numpy import cross, eye
+
+
+from .constants import ATOMIC_NUMBER
+
 
 # Structure of xyz:
 # [<EL>, [x, y, z]]
@@ -375,15 +379,15 @@ def create_derivative(base_xyz, sub_xyz):
 
     anchor = [i for i in range(len(sub_xyz)) if sub_xyz[i][0] == "He"]
     if len(anchor) != 1:
-        print("Invalid substituent: {}".format(sub))
+        print("Invalid substituent")
         return
 
     anchor = anchor[0]
 
     conn = get_neighbors_lists(sub_xyz, He_radius=1.4)
     anchor_neigh = conn[anchor]
     if len(anchor_neigh) != 1:
-        print("Could not find proper substitution bond: {}".format(sub))
+        print("Could not find proper substitution bond")
         return
     sub_neigh = anchor_neigh[0]
 

frontend/management/commands/add_resources.py

@@ -1,9 +1,6 @@
-import os
 from django.core.management.base import BaseCommand
 
-from frontend.models import *
-from frontend.environment_variables import *
-from frontend.tasks import run_calc
+from frontend.models import ResourceAllocation, User
 from frontend.helpers import get_random_string
 
 

frontend/management/commands/check_su.py

@@ -18,7 +18,7 @@
 """
 
 from django.core.management.base import BaseCommand
-from frontend.models import *
+from frontend.models import User, os
 
 su_email = os.environ.get("CALCUS_SU_EMAIL", "")
 

frontend/management/commands/init_static_obj.py

@@ -25,7 +25,15 @@
 filepath = pathlib.Path(__file__).parent.resolve()
 
 showcase_dir = os.path.join(filepath.parent.parent, "showcases")
-from frontend.models import *
+from frontend.models import (
+    BasicStep,
+    Example,
+    Parameters,
+    Recipe,
+    ShowcaseEnsemble,
+    ShowcaseProperty,
+    Structure,
+)
 from frontend.libxyz import format_xyz, parse_multixyz_from_file
 
 try:

frontend/management/commands/refresh_cached_info.py

@@ -17,10 +17,8 @@
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 
-import glob
-import os
 from django.core.management.base import BaseCommand
-from frontend.models import *
+from frontend.models import Project, Profile
 
 
 class Command(BaseCommand):
@@ -62,7 +60,7 @@ def handle(self, *args, **options):
                         running += 1
                     else:
                         completed += 1
-                if o.ensemble != None:
+                if o.ensemble is not None:
                     mol = o.ensemble.parent_molecule
                     if mol is not None:
                         dnum[mol.id] += o.calculation_set.count()

frontend/management/commands/reschedule_calc.py

@@ -1,9 +1,6 @@
-import glob
-import os
 from django.core.management.base import BaseCommand
 
-from frontend.models import *
-from frontend.environment_variables import *
+from frontend.models import Calculation
 from frontend.cloud_job import submit_cloud_job
 
 

frontend/management/commands/run_calc.py

@@ -1,8 +1,7 @@
 import os
 from django.core.management.base import BaseCommand
 
-from frontend.models import *
-from frontend.environment_variables import *
+from frontend.models import Calculation
 from frontend.tasks import run_calc
 
 

frontend/management/commands/wipe.py

@@ -17,10 +17,9 @@
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 
-import glob
 import os
 from django.core.management.base import BaseCommand
-from frontend.models import *
+from frontend.models import Calculation, Molecule, Project
 
 try:
     os.environ["CALCUS_TEST"]