Fixed some problems with CICYs, improved Dockerfile, and bumped to ve…

…rsion 0.3.1

Dockerfile

@@ -1,9 +1,14 @@
 # Start from Debian Bullseye
 FROM debian:bullseye
 
+# Define build arguments
+ARG USERNAME
 ARG USERID
 ARG ARCH
 ARG AARCH
+ARG VIRTUAL_ENV
+ARG ALLOW_ROOT_ARG
+ENV ALLOW_ROOT=$ALLOW_ROOT_ARG
 
 # Install dependencies
 RUN apt-get -yqq update
@@ -12,35 +17,34 @@ RUN apt-get -yqq install autoconf build-essential nano cmake libgmp-dev libcgal-
  libmpc-dev libsuitesparse-dev libppl-dev libeigen3-dev\
  libc6 libcdd0d libgmp10 libgmpxx4ldbl libstdc++6 palp\
  libflint-dev libflint-arb-dev python3 python3-pip\
- cython3 wget libmath-libm-perl
+ wget libmath-libm-perl python3-venv
 
-# Make a soft link for python for convenience
-RUN ln -s /usr/bin/python3 /usr/bin/python
-# Make a soft link to the arb library so that python-flint can install
-RUN echo testt ${AARCH}
+# Make a soft link to the arb library and flint headers so that python-flint can install
 RUN ln -s /usr/lib/${AARCH}-linux-gnu/libflint-arb.so /usr/lib/${AARCH}-linux-gnu/libarb.so
-
-# Fix flint headers
-RUN cp -r /usr/include/flint/* /usr/include/
+RUN ln -s /usr/include/flint/* /usr/include/
 
 # Set up non-root user
-ARG USERID
-RUN groupadd -r -g $USERID cytools && useradd -r -s /bin/bash -u $USERID -g cytools -m cytools
-USER cytools
+RUN groupadd -r -g $USERID $USERNAME && useradd -r -s /bin/bash -u $USERID -g $USERNAME -m $USERNAME\
+ || echo "Skipping user creation"
+USER $USERNAME
+
+# Create python virtual environment for non-root user
+RUN python3 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
 # Install pip packages
 ENV CVXOPT_SUITESPARSE_INC_DIR=/usr/include/suitesparse
 RUN pip3 install --upgrade pip
-RUN pip3 install --no-warn-script-location numpy scipy jupyterlab cvxopt gekko pymongo ortools tqdm
-RUN pip3 install --no-warn-script-location python-flint matplotlib
-RUN pip3 install --no-warn-script-location --user scikit-sparse cysignals gmpy2==2.1.0a4
-RUN pip3 install --no-warn-script-location pplpy
-RUN pip3 install --no-warn-script-location -f https://download.mosek.com/stable/wheel/index.html Mosek
+RUN pip3 install numpy scipy jupyterlab cvxopt gekko pymongo ortools tqdm cython
+RUN pip3 install python-flint matplotlib
+RUN pip3 install scikit-sparse cysignals gmpy2==2.1.0a4
+RUN pip3 install pplpy
+RUN pip3 install -f https://download.mosek.com/stable/wheel/index.html Mosek
 ENV MOSEKLM_LICENSE_FILE=/opt/cytools/external/mosek/mosek.lic
 
 # Fix cvxopt bug
 USER root
-RUN sed -i -e 's/mosek.solsta.near_optimal/ /g' /home/cytools/.local/lib/python3.9/site-packages/cvxopt/coneprog.py
+RUN sed -i -e 's/mosek.solsta.near_optimal/ /g' $VIRTUAL_ENV/lib/python3.9/site-packages/cvxopt/coneprog.py
 
 # Install TOPCOM
 WORKDIR /opt/cytools/external/topcom-mod
@@ -78,9 +82,8 @@ ENV OMP_NUM_THREADS=1
 ENV OPENBLAS_NUM_THREADS=1
 
 # Set entry path
-WORKDIR /home/cytools/mounted_volume
+WORKDIR /home/$USERNAME/mounted_volume
 
 # Start jupyter lab by default
-USER cytools
-ENV PATH="/home/cytools/.local/bin:$PATH"
-CMD jupyter lab --ip 0.0.0.0 --port 2875 --no-browser
+USER $USERNAME
+CMD jupyter lab --ip 0.0.0.0 --port 2875 --no-browser $ALLOW_ROOT

Makefile

@@ -21,7 +21,7 @@ endif
 USERID=$(shell id -u)
 USERIDN=$(shell id -u -n)
 
-.PHONY: all build rebuild install uninstall run pull update test
+.PHONY: all build rebuild install uninstall run pull update test build-with-root-user
 
 all:
  @echo "Please specify an instruction (e.g make build)"
@@ -32,15 +32,19 @@ build:
  false; \
  fi
  @ echo "Building CYTools image for user $(USERIDN)..."
- sudo docker build -t cytools:uid-$(USERID) --build-arg USERID=$(USERID) --build-arg ARCH=$(arch) --build-arg AARCH=$(aarch) .
+ sudo docker build -t cytools:uid-$(USERID) --build-arg USERNAME=cytools\
+ --build-arg USERID=$(USERID) --build-arg ARCH=$(arch) --build-arg AARCH=$(aarch)\
+ --build-arg VIRTUAL_ENV=/home/cytools/cytools-venv/ --build-arg ALLOW_ROOT_ARG=" " .
  @ echo "Successfully built CYTools image for user $(USERIDN)"
 
 rebuild:
  @if [ "$(USERID)" = "0" ]; then \
  echo "Please run make as a non-root user and without sudo!"; \
  false; \
  fi
- sudo docker build --no-cache -t cytools:uid-$(USERID) --build-arg USERID=$(USERID) --build-arg ARCH=$(arch) --build-arg AARCH=$(aarch) .
+ sudo docker build --no-cache -t cytools:uid-$(USERID) --build-arg USERNAME=cytools\
+ --build-arg USERID=$(USERID) --build-arg ARCH=$(arch) --build-arg AARCH=$(aarch)\
+ --build-arg VIRTUAL_ENV=/home/cytools/cytools-venv/ --build-arg ALLOW_ROOT_ARG=" " .
 
 install: build
  @if [ "$(USERID)" = "0" ]; then \
@@ -113,3 +117,17 @@ test: unittests
  false; \
  fi
  sudo docker run --rm -it -v ${PWD}/unittests:/home/cytools/mounted_volume/ cytools bash -c "bash run_tests.sh"
+
+build-with-root-user:
+ @ echo " "
+ @ echo "********************************************************************"
+ @ echo "Warning: You are building an image with a root user. Any user with "
+ @ echo "access to this image will be able to have root access to the host "
+ @ echo "computer as well. Please proceed with care.";
+ @ echo "********************************************************************"
+ @ echo " "
+ @ read -p "Press enter to continue or ctrl+c to cancel"
+ sudo docker build -t cytools:root --build-arg USERNAME=root\
+ --build-arg USERID=0 --build-arg ARCH=$(arch) --build-arg AARCH=$(aarch)\
+ --build-arg VIRTUAL_ENV=/opt/cytools/cytools-venv/ --build-arg ALLOW_ROOT_ARG="--allow-root" .
+ @ echo "Successfully built CYTools image with root user."

cytools/__init__.py

@@ -19,7 +19,7 @@
 from cytools.utils import read_polytopes, fetch_polytopes
 
 # Latest version
-version = "0.3.0"
+version = "0.3.1"
 versions_with_serious_bugs = []
 
 # Check for more recent versions of CYTools

cytools/calabiyau.py

@@ -917,7 +917,7 @@ def glsm_charge_matrix(self, include_origin=True):
  if self._glsm_charge_matrix is not None:
  return np.array(self._glsm_charge_matrix)[:,(0 if include_origin else 1):]
  toric_divs = [0]+list(self.prime_toric_divisors())
- pts = self.ambient_variety().polytope().points_to_indices(self.ambient_variety().triangulation().points()[toric_divs])
+ pts = self.polytope().points_to_indices(self.polytope().points()[toric_divs])
  self._glsm_charge_matrix = self.polytope().glsm_charge_matrix(
  include_origin=True,
  points=pts)
@@ -955,7 +955,7 @@ def glsm_linear_relations(self, include_origin=True):
  if self._glsm_linrels is not None:
  return np.array(self._glsm_linrels)[(0 if include_origin else 1):,(0 if include_origin else 1):]
  toric_divs = [0]+list(self.prime_toric_divisors())
- pts = self.ambient_variety().polytope().points_to_indices(self.ambient_variety().triangulation().points()[toric_divs])
+ pts = self.polytope().points_to_indices(self.polytope().points()[toric_divs])
  self._glsm_linrels = self.polytope().glsm_linear_relations(
  include_origin=True,
  points=pts)
@@ -1003,9 +1003,10 @@ def divisor_basis(self, include_origin=True, as_matrix=False):
  """
  if self._divisor_basis is None:
  self.set_divisor_basis(self.polytope().glsm_basis(
- integral=True,
- include_origin=True,
- points=self.polytope().points_to_indices(self.triangulation().points()))
+ integral=True,
+ include_origin=True,
+ points=self.polytope().points_to_indices(
+ self.polytope().points()[[0]+list(self.prime_toric_divisors())]))
  )
  if len(self._divisor_basis.shape) == 1:
  if 0 in self._divisor_basis and not include_origin:
@@ -1275,6 +1276,24 @@ def intersection_numbers(self, in_basis=False, zero_as_anticanonical=False,
  intnums_cy[ii] = int(round(intnums_cy[ii]))
  else:
  self._is_smooth = False
+ # Now we find the prime toric divisors and reindex accordingly
+ intnum_ind = set.union(*[set(ii) for ii in intnums_cy])
+ triang_inds = sorted(intnum_ind)
+ self._prime_divs = tuple(self.triangulation().triangulation_to_polytope_indices([i for i in triang_inds if i]))
+ divs_dict = {ii:i for i,ii in enumerate(self._prime_divs,1)}
+ divs_dict[0] = 0
+ intnums_cy = {tuple(divs_dict[i] for i in ii):intnums_cy[ii] for ii in intnums_cy}
+ # If there are some non-intersecting divisors we construct a better
+ # toric variety in the background
+ if len(self._prime_divs) == self.ambient_variety().triangulation().points().shape[0]-1:
+ self._optimal_ambient_var = self._ambient_var
+ else:
+ heights = self.triangulation().cpl_cone().tip_of_stretched_cone(1)[triang_inds]
+ try:
+ self._optimal_ambient_var = self.polytope().triangulate(heights=heights, points=self.polytope().points_to_indices(
+ self.polytope().points()[[0]+list(self._prime_divs)])).get_toric_variety()
+ except:
+ raise Exception("This type of complete intersection is not supported.")
  self._intersection_numbers[4*exact_arithmetic] = intnums_cy
  # Now intersection numbers have been computed
  if zero_as_anticanonical and not in_basis:
@@ -1300,14 +1319,17 @@ def prime_toric_divisors(self):
  **Description:**
  Returns the list of inherited prime toric divisors. Due to the sorting
  of points in the polytope class, this list is trivial for
- hypersurfaces, but may be non-trivial for CICYs.
+ hypersurfaces, but may be non-trivial for CICYs. The indices in the
+ returned tuple correspond to indices of the corresponding points of the
+ polytope (i.e. if $n$ is in the tuple, then the $n$th point in
+ ```p.points()``` is a prime toric divisor that intersects the CY).
 
  **Arguments:**
  None
 
  **Returns:**
- *(tuple)* A list of indices indicating the prime toric divisors of the
- ambient variety that intersect the CY.
+ *(tuple)* A list of indices indicating the points in the polytope whose
+ corresponding prime toric divisor intersects the CY.
 
  **Example:**
  We construct a Calabi-Yau hypersurface and find the list of prime toric
@@ -1322,16 +1344,13 @@ def prime_toric_divisors(self):
  """
  if self._prime_divs is not None:
  return self._prime_divs
- intnum_ind = set.union(*[set(ii) for ii in self.intersection_numbers()])
- self._prime_divs = tuple(i for i in intnum_ind if i)
- # If there are some non-intersecting divisors we construct a better
- # toric variety in the background
- if len(self._prime_divs) == self.ambient_variety().triangulation().points().shape[0]-1:
+ if self._is_hypersurface:
+ self._prime_divs = tuple(range(1,self.polytope().points_not_interior_to_facets().shape[0]))
  self._optimal_ambient_var = self._ambient_var
  else:
- heights = self._ambient_var.mori_cone().dual().tip_of_stretched_cone(1)[[0]+list(self._prime_divs)]
- self._optimal_ambient_var = self.polytope().triangulate(heights=heights, points=self.polytope().points_to_indices(
-  self.ambient_variety().triangulation().points()[[0]+list(self._prime_divs)])).get_toric_variety()
+ # For CICYs we have to compute intersection numbers and the
+ # variables are set during the computation
+ self.intersection_numbers()
  return self._prime_divs
 
  def second_chern_class(self, in_basis=False):

scripts/linux/cytools

@@ -106,7 +106,7 @@ cat << EOF
  ░░█████████ █████ █████ ░░██████ ░░██████ █████ ██████
  ░░░░░░░░░ ░░░░░ ░░░░░ ░░░░░░ ░░░░░░ ░░░░░ ░░░░░░
 
- Developed by Liam McAllister's Group | Version 0.3.0
+ Developed by Liam McAllister's Group | Version 0.3.1
  https://cytools.liammcallistergroup.com
 
 EOF

scripts/macos/cytools

@@ -100,7 +100,7 @@ cat << EOF
  ░░█████████ █████ █████ ░░██████ ░░██████ █████ ██████
  ░░░░░░░░░ ░░░░░ ░░░░░ ░░░░░░ ░░░░░░ ░░░░░ ░░░░░░
 
- Developed by Liam McAllister's Group | Version 0.3.0
+ Developed by Liam McAllister's Group | Version 0.3.1
  https://cytools.liammcallistergroup.com
 
 EOF

scripts/windows/install.bat

@@ -2,11 +2,9 @@
 
 set PWS=powershell.exe -ExecutionPolicy Bypass -NoLogo -NoProfile
 
-%PWS% -File "%~p0%fixdockerfile.ps1"
-
 docker info || echo. && echo "Please make sure that Docker is installed and running" && timeout /t 10 && exit
 
-docker build -t cytools --build-arg USERID=1000 --build-arg ARCH=amd64 --build-arg AARCH=x86_64 ../../ || echo. && echo "There was an error while building the image. Please let the developers know, and try using a stable version of the package." && timeout /t 10 && exit
+docker build -t cytools --build-arg USERNAME=root --build-arg USERID=0 --build-arg ARCH=amd64 --build-arg AARCH=x86_64 --build-arg VIRTUAL_ENV=/opt/cytools/cytools-venv/ --build-arg ALLOW_ROOT_ARG="--allow-root" ../../ || echo. && echo "There was an error while building the image. Please let the developers know, and try using a stable version of the package." && timeout /t 10 && exit
 
 set TARGET="%appdata%\CYTools\cytools.bat"
 set TARGETU="%appdata%\CYTools\uninstall.bat"

scripts/windows/launcher.ps1

@@ -38,7 +38,7 @@ $banner=@"
  ░░█████████ █████ █████ ░░██████ ░░██████ █████ ██████
  ░░░░░░░░░ ░░░░░ ░░░░░ ░░░░░░ ░░░░░░ ░░░░░ ░░░░░░
 
- Developed by Liam McAllister's Group | Version 0.3.0
+ Developed by Liam McAllister's Group | Version 0.3.1
  https://cytools.liammcallistergroup.com
 
 "@

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
  name="cytools",
- version="0.3.0",
+ version="0.3.1",
  author="Liam McAllister Group",
  author_email="",
  description="A software package for analyzing Calabi-Yau hypersurfaces in toric varieties.",