Fixed Docker and various updates to functions

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.gitignore

@@ -1,3 +1,6 @@
 /Manifest.toml
 .vscode/settings.json
 src/clipboard.jl
+jlm_python/multi_solver_phase_fraction.py
+jlm_python/one_dim_phase_fraction.py
+.DS_Store

Dockerfile

@@ -18,8 +18,8 @@ RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata
 RUN apt-get -yqq install autoconf build-essential nano cmake libgmp-dev libcgal-dev\
                          libmpc-dev libsuitesparse-dev libppl-dev libeigen3-dev\
                          libc6 libcdd0d libgmp10 libgmpxx4ldbl libstdc++6 palp\
-                         libflint-dev libflint-arb-dev python3 python3-pip\
-                         wget libmath-libm-perl python3-venv normaliz git
+                         libflint-dev libflint-arb-dev python3 python3-pip curl\
+                         wget libmath-libm-perl python3-venv normaliz libqsopt-ex2 git
 
 # 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
@@ -30,27 +30,35 @@ RUN groupadd -r -g $USERID $USERNAME && useradd -r -s /bin/bash -u $USERID -g $U
     || echo "Skipping user creation"
 USER $USERNAME
 
+# Install Rust since there are some Python packages that now depend on it
+RUN curl https://sh.rustup.rs -sSf | bash -s -- -y
+ENV PATH="/home/${USERNAME}/.cargo/bin:${PATH}"
+
 # Create python virtual environment for non-root user
 RUN python3 -m venv $VIRTUAL_ENV
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
 # Install julia 
 WORKDIR /opt/cytools/
-RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.7/julia-1.7.1-linux-x86_64.tar.gz
-RUN tar xf julia-1.7.1-linux-x86_64.tar.gz
-ENV PATH="$PWD/julia-1.7.1/bin:$PATH"
-RUN ln -s $PWD/julia-1.7.1/bin/julia $VIRTUAL_ENV/bin/julia
-RUN rm julia-1.7.1-linux-x86_64.tar.gz
-
+RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.4-linux-x86_64.tar.gz
+RUN tar xf julia-1.8.4-linux-x86_64.tar.gz
+ENV PATH="$PWD/julia-1.8.4/bin:$PATH"
+RUN ln -s $PWD/julia-1.8.4/bin/julia $VIRTUAL_ENV/bin/julia
+RUN rm julia-1.8.4-linux-x86_64.tar.gz
+# RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.7/julia-1.7.1-linux-x86_64.tar.gz
+# RUN tar xf julia-1.7.1-linux-x86_64.tar.gz
+# ENV PATH="$PWD/julia-1.7.1/bin:$PATH"
+# RUN ln -s $PWD/julia-1.7.1/bin/julia $VIRTUAL_ENV/bin/julia
+# RUN rm julia-1.7.1-linux-x86_64.tar.gz
 
+# Install pip packages
 # Install pip packages
 ENV CVXOPT_SUITESPARSE_INC_DIR=/usr/include/suitesparse
-RUN pip3 install --upgrade pip
+RUN pip3 install pip==21.0.1
 RUN pip3 install numpy scipy jupyterlab cvxopt gekko pymongo ortools tqdm cython qpsolvers osqp
 RUN pip3 install python-flint matplotlib h5py
-RUN pip3 install scikit-sparse cysignals gmpy2==2.1.0a4
+RUN pip3 install scikit-sparse cysignals gmpy2
 RUN pip3 install pplpy
-RUN pip3 install julia
 RUN pip3 install -f https://download.mosek.com/stable/wheel/index.html Mosek
 ENV MOSEKLM_LICENSE_FILE=/home/$USERNAME/mounted_volume/mosek/mosek.lic
 
@@ -60,8 +68,15 @@ RUN sed -i -e 's/mosek.solsta.near_optimal/ /g' $VIRTUAL_ENV/lib/python3.9/site-
 
 # Install TOPCOM
 WORKDIR /opt/cytools/external/topcom-mod
-RUN wget https://github.com/LiamMcAllisterGroup/topcom/releases/download/v0.17.8%2Bds-2%2Bcytools-1/topcom_0.17.8+ds-2+cytools-1_${ARCH}.deb
-RUN dpkg -i topcom_0.17.8+ds-2+cytools-1_${ARCH}.deb
+RUN wget https://github.com/LiamMcAllisterGroup/topcom/releases/download/v1.1.2%2Bds-1%2Bcytools-1/topcom_1.1.2+ds-1+cytools-1_${ARCH}.deb
+RUN wget https://github.com/LiamMcAllisterGroup/topcom/releases/download/v1.1.2%2Bds-1%2Bcytools-1/libtopcom0_1.1.2+ds-1+cytools-1_${ARCH}.deb
+RUN wget https://github.com/LiamMcAllisterGroup/topcom/releases/download/v1.1.2%2Bds-1%2Bcytools-1/libtopcom-dev_1.1.2+ds-1+cytools-1_${ARCH}.deb
+RUN dpkg -i topcom_1.1.2+ds-1+cytools-1_${ARCH}.deb
+RUN dpkg -i libtopcom0_1.1.2+ds-1+cytools-1_${ARCH}.deb
+RUN dpkg -i libtopcom-dev_1.1.2+ds-1+cytools-1_${ARCH}.deb
+
+# Download file from github to keep track of the number of downloads
+RUN wget https://github.com/LiamMcAllisterGroup/cytools/releases/download/v1.0.0/download_counter.txt
 
 # Copy code and installer
 COPY . /opt/cytools/
@@ -70,7 +85,7 @@ RUN python3 setup.py install
 
 # Copy CYAxiverse.jl package
 WORKDIR /opt/
-RUN git clone -b dev https://github.com/vmmhep/CYAxiverse.jl.git
+RUN git clone -b vmm https://github.com/Julia-meets-String-Theory/CYAxiverse.jl.git
 WORKDIR /opt/CYAxiverse.jl/
 ENV PYTHON="$VIRTUAL_ENV/bin/python3"
 RUN julia --project="/opt/CYAxiverse.jl/" add_CYAxiverse.jl
@@ -103,6 +118,7 @@ WORKDIR /home/$USERNAME/mounted_volume
 
 # Start jupyter lab by default
 USER $USERNAME
+
 ENV JULIA_REVISE_POLL=1
 EXPOSE 8996
 ENV newARGS="docker"

LICENSE

@@ -19,3 +19,24 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+MIT License
+
+Copyright (c) 2022 vmmhep
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Project.toml

@@ -9,8 +9,11 @@ ArbNumerics = "7e558dbc-694d-5a72-987c-6f4ebed21442"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 ClusterManagers = "34f1f09b-3a8b-5176-ab39-66d58a4d544e"
+ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
@@ -19,30 +22,59 @@ DrWatson = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 GenericLinearAlgebra = "14197337-ba66-59df-a3e3-ca00e7dcff7a"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
 IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807"
+LeftChildRightSiblingTrees = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e"
 LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 MPIClusterManagers = "e7922434-ae4b-11e9-05c5-9780451d2c66"
 MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a"
+NormalForms = "109d20d8-9763-411c-9b60-7eb2a068657f"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
 ProfileSVG = "132c30aa-f267-4189-9183-c8a63c7e05e6"
 ProgressLogging = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+QRCoders = "f42e9828-16f3-11ed-2883-9126170b272d"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 SharedArrays = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Tullio = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"
 
 [compat]
 julia = "1.7"
+AbstractTrees = "=0.4.3"
+ArbNumerics = "=1.3.3"
+BenchmarkTools = "=1.3.2"
+CairoMakie = "=0.10.0"
+ClusterManagers = "=0.4.3"
+ColorSchemes = "=3.20.0"
+Conda = "=1.7.0"
+DifferentialEquations = "=7.7.0"
+Distributions = "=0.25.60"
+Documenter = "=0.27.20"
+DrWatson = "=2.12.0"
+ForwardDiff = "=0.10.32"
+GenericLinearAlgebra = "=0.3.3"
+HDF5 = "=0.16.11"
+IntervalArithmetic = "=0.20.7"
+LoopVectorization = "=0.12.140"
+MPI = "=0.20.0"
+Nemo = "=0.32.0"
+NormalForms = "=0.1.0"
+Optim = "=1.7.0"
+Roots = "=2.0.0"
+Tullio = "=0.3.4"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"