From c95c726a2ba029e5b6a11434708d59c15c82b8a7 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Wed, 27 Aug 2025 00:39:50 -0400
Subject: [PATCH 01/46] fix compatibility with pyscf 2.0.1 by explicitly
 writing the unique_with_wrap_around function

---
 python/green_igen/df.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/python/green_igen/df.py b/python/green_igen/df.py
index a575204..5fb27dc 100644
--- a/python/green_igen/df.py
+++ b/python/green_igen/df.py
@@ -52,9 +52,7 @@
 from pyscf.pbc.df import df_ao2mo
 from pyscf.pbc.df.aft import get_nuc
 from pyscf.pbc.df.df_jk import zdotCN
-from pyscf.pbc.lib.kpts_helper import (is_zero, gamma_point, member, unique, unique_with_wrap_around,
-                                       KPT_DIFF_TOL)
-from pyscf.pbc.df.aft import _sub_df_jk_
+from pyscf.pbc.lib.kpts_helper import (is_zero, gamma_point, member, unique, KPT_DIFF_TOL)
 from pyscf import __config__
 
 LINEAR_DEP_THR = getattr(__config__, 'pbc_df_df_DF_lindep', 1e-9)
@@ -66,6 +64,19 @@
 # cutoff penalty due to lattice summation
 LATTICE_SUM_PENALTY = 1e-1
 
+
+def unique_with_wrap_around(cell, kpts):
+    '''Search unique kpts in first Brillouin zone.'''
+    scaled_kpts = cell.get_scaled_kpts(kpts).round(5)
+    scaled_kpts = numpy.modf(scaled_kpts)[0]
+    scaled_kpts[scaled_kpts >= .5] -= 1
+    scaled_kpts[scaled_kpts < -.5] += 1
+
+    uniq_index, uniq_inverse = unique(scaled_kpts)[1:3]
+    uniq_kpts = kpts[uniq_index]
+    return uniq_kpts, uniq_index, uniq_inverse
+
+
 def make_auxmol(mol, auxbasis):
     '''Generate a fake Mole object which uses the density fitting auxbasis as
     the basis sets.  If auxbasis is not specified, the optimized auxiliary fitting

From 13adf37bca7b2f407735cbce5eaf8cef2dda9504 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 17:13:19 -0400
Subject: [PATCH 02/46] Create python-package.yml

Add testing for specific versions of PySCF for compatibility of green-mbtools with green-igen
---
 .github/workflows/python-package.yml | 50 ++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 .github/workflows/python-package.yml

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
new file mode 100644
index 0000000..b5af7ff
--- /dev/null
+++ b/.github/workflows/python-package.yml
@@ -0,0 +1,50 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        pyscf-paths: ["https://github.com/cnyeh/pyscf.git@x2c1e_kpoints", "https://github.com/pyscf/pyscf.git"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        pip install git+${{ pyscf-paths }}
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Install package
+      run: |
+        pip install .
+    - name: Install Green-MBTools
+      run: |
+        pip install green-mbtools
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test Green-MBTools with pytest
+      run: |
+        git clone https://github.com/green-phys/green-mbtools
+        cd green-mbtools/tests
+        pytest -v

From ae2e7340e675a6cf725f0bd8b6c626b1152c1f82 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 17:16:13 -0400
Subject: [PATCH 03/46] Update python-package.yml

---
 .github/workflows/python-package.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index b5af7ff..3f89b8c 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
-        pyscf-paths: ["https://github.com/cnyeh/pyscf.git@x2c1e_kpoints", "https://github.com/pyscf/pyscf.git"]
+        pyscf-version: ["https://github.com/cnyeh/pyscf.git@x2c1e_kpoints", "https://github.com/pyscf/pyscf.git"]
 
     steps:
     - uses: actions/checkout@v4
@@ -29,7 +29,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        pip install git+${{ pyscf-paths }}
+        pip install git+${{ pyscf-version }}
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install package
       run: |

From 0e44adbff2abb190961e8feec08185492b1a5af5 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 17:20:15 -0400
Subject: [PATCH 04/46] debug python-project.yml

---
 .github/workflows/python-package.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 3f89b8c..c47a77a 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -17,7 +17,9 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
-        pyscf-version: ["https://github.com/cnyeh/pyscf.git@x2c1e_kpoints", "https://github.com/pyscf/pyscf.git"]
+        pyscf-version:
+          - "https://github.com/cnyeh/pyscf.git@x2c1e_kpoints"
+          - "https://github.com/pyscf/pyscf.git"
 
     steps:
     - uses: actions/checkout@v4
@@ -29,7 +31,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        pip install git+${{ pyscf-version }}
+        pip install git+${{ matrix.pyscf-version }}
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install package
       run: |

From dda25ebc5516abc80bdf06af5b40613dc066a9a5 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 17:22:27 -0400
Subject: [PATCH 05/46] update python app test dependencies

---
 .github/workflows/python-package.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index c47a77a..fc1814f 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -29,6 +29,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
+        sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
         pip install git+${{ matrix.pyscf-version }}

From e91e73629a5afcf4e4ab03672465744071473f45 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 17:35:37 -0400
Subject: [PATCH 06/46] disable linting

---
 .github/workflows/python-package.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index fc1814f..2e09742 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -40,12 +40,12 @@ jobs:
     - name: Install Green-MBTools
       run: |
         pip install green-mbtools
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    # - name: Lint with flake8
+    #   run: |
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test Green-MBTools with pytest
       run: |
         git clone https://github.com/green-phys/green-mbtools

From c00b48ee05e18f3b4537222c29732652720564ed Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 18:23:37 -0400
Subject: [PATCH 07/46] add scipy version that satisfies new and old pyscf
 linalg_helper

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 9cf44d9..bffbcd6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 numpy
-scipy
+scipy=1.7.0
 h5py
 pyscf
\ No newline at end of file

From 93d7c41e9d0ef294189c5c85bd8efe4929fae4c6 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 18:23:56 -0400
Subject: [PATCH 08/46] update version number

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index da54c9d..12443c0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ cmake.verbose = true
 
 [project]
 name = "green-igen"
-version = "0.2.6"
+version = "0.2.7"
 authors = [
   { name="Sergei Iskakov", email="siskakov@umich.edu" },
 ]

From e92795b19a3f82878fbdd22a9c9c2536cd3b37cc Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 18:49:20 -0400
Subject: [PATCH 09/46] modify scipy dependencies and order of python package
 testing

---
 .github/workflows/python-package.yml | 2 +-
 requirements.txt                     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 2e09742..fd194aa 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -32,8 +32,8 @@ jobs:
         sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        pip install git+${{ matrix.pyscf-version }}
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install git+${{ matrix.pyscf-version }}
     - name: Install package
       run: |
         pip install .
diff --git a/requirements.txt b/requirements.txt
index bffbcd6..e0cc481 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 numpy
-scipy=1.7.0
+scipy<=1.16.0
 h5py
 pyscf
\ No newline at end of file

From a7f0119b0888f91c475afbca8d6d77e1b103d29f Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 23:23:14 -0400
Subject: [PATCH 10/46] fix python package testing workflow

---
 .github/workflows/python-package.yml | 3 ++-
 requirements.txt                     | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index fd194aa..2daa907 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -30,8 +30,9 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev
+        sudo apt-get install build-essential libm-dev
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install flake8 pytest 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install git+${{ matrix.pyscf-version }}
     - name: Install package
diff --git a/requirements.txt b/requirements.txt
index e0cc481..e999f51 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 numpy
-scipy<=1.16.0
+scipy<1.11.0
 h5py
 pyscf
\ No newline at end of file

From aab27380de5d6f29d5356bda689cdced3d9cbb0f Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 23:26:04 -0400
Subject: [PATCH 11/46] same old - fix workflow

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 2daa907..b2cfdbc 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -30,7 +30,7 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev
-        sudo apt-get install build-essential libm-dev
+        sudo apt-get install build-essential
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

From 36f59a187e4e0b3c1618faa5ca275deb3c87e097 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 30 Aug 2025 23:49:36 -0400
Subject: [PATCH 12/46] workflow tweaks

---
 .github/workflows/python-package.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index b2cfdbc..dc89dd7 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -18,8 +18,8 @@ jobs:
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
         pyscf-version:
-          - "https://github.com/cnyeh/pyscf.git@x2c1e_kpoints"
-          - "https://github.com/pyscf/pyscf.git"
+          - "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints"
+          - "pyscf==2.7.0"
 
     steps:
     - uses: actions/checkout@v4
@@ -30,14 +30,14 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev
-        sudo apt-get install build-essential
+        sudo apt install build-essential
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install git+${{ matrix.pyscf-version }}
+        pip install ${{ matrix.pyscf-version }}
     - name: Install package
       run: |
-        pip install .
+        python -m pip install .
     - name: Install Green-MBTools
       run: |
         pip install green-mbtools
@@ -50,5 +50,6 @@ jobs:
     - name: Test Green-MBTools with pytest
       run: |
         git clone https://github.com/green-phys/green-mbtools
+        python -c "import scipy; print(scipy.__version__)"
         cd green-mbtools/tests
         pytest -v

From e1d9e2791ee03cc718108d4b17da3c76526fd6d3 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 00:29:22 -0400
Subject: [PATCH 13/46] control testing workflow dependencies

---
 .github/workflows/python-package.yml | 6 +++---
 pyproject.toml                       | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index dc89dd7..d837cd5 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -29,12 +29,12 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev
+        sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev libhdf5-dev
         sudo apt install build-essential
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest 
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install ${{ matrix.pyscf-version }}
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install package
       run: |
         python -m pip install .
@@ -50,6 +50,6 @@ jobs:
     - name: Test Green-MBTools with pytest
       run: |
         git clone https://github.com/green-phys/green-mbtools
-        python -c "import scipy; print(scipy.__version__)"
+        python -c "import scipy; print("Scipy version: ", scipy.__version__)"
         cd green-mbtools/tests
         pytest -v
diff --git a/pyproject.toml b/pyproject.toml
index 12443c0..4c9f538 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,9 +12,10 @@ name = "green-igen"
 version = "0.2.7"
 authors = [
   { name="Sergei Iskakov", email="siskakov@umich.edu" },
+  { name="Gaurav Harsha" },
 ]
 
-dependencies = ["numpy", "h5py", "scipy", "pyscf"]
+dependencies = ["numpy", "h5py", "scipy<1.11.0", "pyscf"]
 
 description = "Analytical continuation suits for Green Software Package"
 readme = "README.md"

From 4fd426140e71f637f8d7408bf3a8a5287de3f7a9 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 00:34:50 -0400
Subject: [PATCH 14/46] fix typo in workflow

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index d837cd5..cd2df3c 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -50,6 +50,6 @@ jobs:
     - name: Test Green-MBTools with pytest
       run: |
         git clone https://github.com/green-phys/green-mbtools
-        python -c "import scipy; print("Scipy version: ", scipy.__version__)"
+        python -c "import scipy; print('Scipy version: ', scipy.__version__)"
         cd green-mbtools/tests
         pytest -v

From 0cb2baf98bc2bfbfc349b247672b78aba9ff8ff8 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 00:53:34 -0400
Subject: [PATCH 15/46] scipy version fix

---
 .github/workflows/python-package.yml | 4 ++--
 pyproject.toml                       | 2 +-
 requirements.txt                     | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index cd2df3c..bee39c8 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -33,14 +33,14 @@ jobs:
         sudo apt install build-essential
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest 
-        pip install ${{ matrix.pyscf-version }}
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
     - name: Install package
       run: |
         python -m pip install .
     - name: Install Green-MBTools
       run: |
-        pip install green-mbtools
+        pip install --upgrade-strategy only-if-needed green-mbtools
     # - name: Lint with flake8
     #   run: |
     #     # stop the build if there are Python syntax errors or undefined names
diff --git a/pyproject.toml b/pyproject.toml
index 4c9f538..85a0f4e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ authors = [
   { name="Gaurav Harsha" },
 ]
 
-dependencies = ["numpy", "h5py", "scipy<1.11.0", "pyscf"]
+dependencies = ["numpy", "h5py", "scipy>=1.10,<1.11.0", "pyscf"]
 
 description = "Analytical continuation suits for Green Software Package"
 readme = "README.md"
diff --git a/requirements.txt b/requirements.txt
index e999f51..8a829dd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 numpy
-scipy<1.11.0
+scipy>=1.10,<1.11.0
 h5py
 pyscf
\ No newline at end of file

From 5332d6f2476112d154b8fc817b5e41fcb467da59 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 01:43:32 -0400
Subject: [PATCH 16/46] scipy compatibility in linalg_helper.py

---
 python/green_igen/linalg_helper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/green_igen/linalg_helper.py b/python/green_igen/linalg_helper.py
index e1354f4..2784af5 100644
--- a/python/green_igen/linalg_helper.py
+++ b/python/green_igen/linalg_helper.py
@@ -1478,7 +1478,7 @@ def cho_solve(a, b, strict_sym_pos=True):
             on matrix a
     '''
     try:
-        return scipy.linalg.solve(a, b, sym_pos=True)
+        return scipy.linalg.solve(a, b, assume_a=True)
     except numpy.linalg.LinAlgError:
         if strict_sym_pos:
             raise

From 5581bd928498eef9f5ce6d1cbc201c36d74c6af3 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 01:43:54 -0400
Subject: [PATCH 17/46] modify python package testing workflow

---
 .github/workflows/python-package.yml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index bee39c8..1ee4fc6 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -38,18 +38,17 @@ jobs:
     - name: Install package
       run: |
         python -m pip install .
-    - name: Install Green-MBTools
+    - name: Install Green-MBTools and Test igen
       run: |
-        pip install --upgrade-strategy only-if-needed green-mbtools
+        git clone https://github.com/green-phys/green-mbtools
+        cd green-mbtools
+        pip install --upgrade-strategy only-if-needed .
+        python -c "import scipy; print('Scipy version: ', scipy.__version__)"
+        cd tests
+        pytest -v
     # - name: Lint with flake8
     #   run: |
     #     # stop the build if there are Python syntax errors or undefined names
     #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
     #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
     #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test Green-MBTools with pytest
-      run: |
-        git clone https://github.com/green-phys/green-mbtools
-        python -c "import scipy; print('Scipy version: ', scipy.__version__)"
-        cd green-mbtools/tests
-        pytest -v

From c7d1e8ff1842e11078e1f2b5326828a30ebbcb9e Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 12:27:43 -0400
Subject: [PATCH 18/46] remove control over scipy in requirements

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 8a829dd..9cf44d9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 numpy
-scipy>=1.10,<1.11.0
+scipy
 h5py
 pyscf
\ No newline at end of file

From cdc81180643c2b696ab9e60bdac1e788aea25f7e Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 13:02:36 -0400
Subject: [PATCH 19/46] update workflow file

---
 .github/workflows/python-package.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 1ee4fc6..74c85f4 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -35,9 +35,12 @@ jobs:
         python -m pip install flake8 pytest 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
+        if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ] then
+          pip install --upgrade scipy<1.11.0
+        fi
     - name: Install package
       run: |
-        python -m pip install .
+        python -m pip install --upgrade-strategy only-if-needed .
     - name: Install Green-MBTools and Test igen
       run: |
         git clone https://github.com/green-phys/green-mbtools

From 5bffdfc08e4206bb7c1f2646dd3f40deaa4cf7b3 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 13:10:12 -0400
Subject: [PATCH 20/46] re-edit pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 85a0f4e..6d91c47 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ authors = [
   { name="Gaurav Harsha" },
 ]
 
-dependencies = ["numpy", "h5py", "scipy>=1.10,<1.11.0", "pyscf"]
+dependencies = ["numpy", "h5py", "scipy", "pyscf"]
 
 description = "Analytical continuation suits for Green Software Package"
 readme = "README.md"

From bd39893260b2cbc09453af075d996e3fad745ea4 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sun, 31 Aug 2025 13:15:43 -0400
Subject: [PATCH 21/46] fix if condition in workflow

---
 .github/workflows/python-package.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 74c85f4..6b4f236 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -35,8 +35,8 @@ jobs:
         python -m pip install flake8 pytest 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
-        if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ] then
-          pip install --upgrade scipy<1.11.0
+        if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
+          pip install --upgrade scipy<1.11.0;
         fi
     - name: Install package
       run: |

From 8c9d8ce50d378a2cef5c3daeee435321cbec4fcf Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Tue, 9 Sep 2025 16:39:34 -0400
Subject: [PATCH 22/46] updates to fix tests in Github

---
 .github/workflows/python-package.yml | 2 +-
 src/CMakeLists.txt                   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 6b4f236..2d3d05f 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -36,7 +36,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
-          pip install --upgrade scipy<1.11.0;
+          pip install --upgrade "scipy<1.11.0";
         fi
     - name: Install package
       run: |
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 81208c6..17df650 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -36,4 +36,4 @@ set_target_properties(pbc0 PROPERTIES
   COMPILE_FLAGS ${OpenMP_C_FLAGS}
   LINK_FLAGS ${OpenMP_C_FLAGS})
 
-target_link_libraries(pbc0 ${BLAS_LIBRARIES})
+target_link_libraries(pbc0 ${BLAS_LIBRARIES} m)

From 1b0575fe25111d6b6e7ad7b75d23d86d4e5332fe Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Wed, 10 Sep 2025 15:15:35 -0400
Subject: [PATCH 23/46] resolve scipy discrepancy

---
 .github/workflows/python-package.yml | 6 +++---
 src/CMakeLists.txt                   | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 2d3d05f..a483dbc 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -35,9 +35,6 @@ jobs:
         python -m pip install flake8 pytest 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
-        if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
-          pip install --upgrade "scipy<1.11.0";
-        fi
     - name: Install package
       run: |
         python -m pip install --upgrade-strategy only-if-needed .
@@ -46,6 +43,9 @@ jobs:
         git clone https://github.com/green-phys/green-mbtools
         cd green-mbtools
         pip install --upgrade-strategy only-if-needed .
+        if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
+          pip install --upgrade "scipy<1.11.0";
+        fi
         python -c "import scipy; print('Scipy version: ', scipy.__version__)"
         cd tests
         pytest -v
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 17df650..81208c6 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -36,4 +36,4 @@ set_target_properties(pbc0 PROPERTIES
   COMPILE_FLAGS ${OpenMP_C_FLAGS}
   LINK_FLAGS ${OpenMP_C_FLAGS})
 
-target_link_libraries(pbc0 ${BLAS_LIBRARIES} m)
+target_link_libraries(pbc0 ${BLAS_LIBRARIES})

From 3178a4cec9e46d55045eba8d6cafef84447303c4 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Wed, 10 Sep 2025 15:41:02 -0400
Subject: [PATCH 24/46] for older pyscf, downgrade scs and cvxpy versions

---
 .github/workflows/python-package.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index a483dbc..8de41cd 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -35,6 +35,10 @@ jobs:
         python -m pip install flake8 pytest 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
+        if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
+          pip install --upgrade "scipy<1.11.0";
+          pip install --upgrade-strategy only-if-needed cvxpy<1.4 scs<3.0
+        fi
     - name: Install package
       run: |
         python -m pip install --upgrade-strategy only-if-needed .
@@ -43,9 +47,6 @@ jobs:
         git clone https://github.com/green-phys/green-mbtools
         cd green-mbtools
         pip install --upgrade-strategy only-if-needed .
-        if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
-          pip install --upgrade "scipy<1.11.0";
-        fi
         python -c "import scipy; print('Scipy version: ', scipy.__version__)"
         cd tests
         pytest -v

From f32dfe8df330ada81fc95d63567b3e56faeca4b9 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Wed, 10 Sep 2025 17:33:28 -0400
Subject: [PATCH 25/46] update scipy installation for pyscf 2.0.1

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 8de41cd..8c7627c 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -37,7 +37,7 @@ jobs:
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
-          pip install --upgrade-strategy only-if-needed cvxpy<1.4 scs<3.0
+          pip install --upgrade-strategy only-if-needed "cvxpy<1.4" "scs<3.0";
         fi
     - name: Install package
       run: |

From ab413de2b2375c8dba9eff12feea69d76a49aff0 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Wed, 10 Sep 2025 17:46:16 -0400
Subject: [PATCH 26/46] modify installation of requirements

---
 .github/workflows/python-package.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 8c7627c..e4ee321 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -32,8 +32,7 @@ jobs:
         sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev libhdf5-dev
         sudo apt install build-essential
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest 
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install flake8 pytest numpy h5py
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
@@ -44,11 +43,11 @@ jobs:
         python -m pip install --upgrade-strategy only-if-needed .
     - name: Install Green-MBTools and Test igen
       run: |
-        git clone https://github.com/green-phys/green-mbtools
-        cd green-mbtools
-        pip install --upgrade-strategy only-if-needed .
+        pip install --upgrade-strategy only-if-needed green-mbtools
         python -c "import scipy; print('Scipy version: ', scipy.__version__)"
-        cd tests
+        cd ../
+        git clone https://github.com/green-phys/green-mbtools
+        cd green-mbtools/tests
         pytest -v
     # - name: Lint with flake8
     #   run: |

From 8b70e7ff81d858fa06dcbb96c8d898fbee1e4a84 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Wed, 10 Sep 2025 18:10:52 -0400
Subject: [PATCH 27/46] one more try to fix link and installation checks

---
 .github/workflows/python-package.yml | 2 +-
 src/CMakeLists.txt                   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index e4ee321..07a2348 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -36,7 +36,7 @@ jobs:
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
-          pip install --upgrade-strategy only-if-needed "cvxpy<1.4" "scs<3.0";
+          pip install --upgrade-strategy only-if-needed "cvxpy<1.4" "scs==3.0";
         fi
     - name: Install package
       run: |
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 81208c6..17df650 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -36,4 +36,4 @@ set_target_properties(pbc0 PROPERTIES
   COMPILE_FLAGS ${OpenMP_C_FLAGS}
   LINK_FLAGS ${OpenMP_C_FLAGS})
 
-target_link_libraries(pbc0 ${BLAS_LIBRARIES})
+target_link_libraries(pbc0 ${BLAS_LIBRARIES} m)

From 1d265b25ac9c57dcffeb10b7830bcfa3cbbef681 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 14:04:27 -0400
Subject: [PATCH 28/46] fix scs version for workflow

---
 .github/workflows/python-package.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 07a2348..f66c674 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -19,7 +19,7 @@ jobs:
         python-version: ["3.9", "3.10", "3.11"]
         pyscf-version:
           - "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints"
-          - "pyscf==2.7.0"
+          - "pyscf"
 
     steps:
     - uses: actions/checkout@v4
@@ -29,14 +29,14 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev liblapack-dev libblas-dev libhdf5-dev
+        sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
         sudo apt install build-essential
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest numpy h5py
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
-          pip install --upgrade-strategy only-if-needed "cvxpy<1.4" "scs==3.0";
+          pip install --upgrade-strategy only-if-needed "cvxpy<1.4" "scs>=3.0.1,<3.1";
         fi
     - name: Install package
       run: |

From 9c86e05da50244e65e114be74cefb56753bd7242 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 16:02:27 -0400
Subject: [PATCH 29/46] reintroduce lapack and blas

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index f66c674..b8f4166 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -29,7 +29,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
+        sudo apt install libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
         sudo apt install build-essential
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest numpy h5py

From 01dac924285307e9026b12b2da1d4cb531bc95db Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 17:17:29 -0400
Subject: [PATCH 30/46] fix distutils error

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index b8f4166..290bb1b 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -29,7 +29,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
+        sudo apt install python3-distutils libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
         sudo apt install build-essential
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest numpy h5py

From 874416721394eab2be10fcc620dac9363d3c5270 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 17:30:12 -0400
Subject: [PATCH 31/46] handle distutils dependency

---
 .github/workflows/python-package.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 290bb1b..5874e5d 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -29,8 +29,15 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
+        sudo apt update
         sudo apt install python3-distutils libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
         sudo apt install build-essential
+        # The following handles distutils for multiple Python versions
+        PY_VER=$(python3 -c "import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')")
+        if ! python3 -c "import distutils" 2>/dev/null; then
+          sudo apt install -y python${PY_VER}-distutils || true
+        fi
+        python -m pip install --upgrade pip setuptools
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest numpy h5py
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}

From c8682fa7426e49f1e054e21f321551602531cebc Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 17:42:55 -0400
Subject: [PATCH 32/46] remove copilot's faulty suggestions

---
 .github/workflows/python-package.yml | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 5874e5d..0e37d11 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -32,22 +32,17 @@ jobs:
         sudo apt update
         sudo apt install python3-distutils libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
         sudo apt install build-essential
-        # The following handles distutils for multiple Python versions
-        PY_VER=$(python3 -c "import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')")
-        if ! python3 -c "import distutils" 2>/dev/null; then
-          sudo apt install -y python${PY_VER}-distutils || true
-        fi
         python -m pip install --upgrade pip setuptools
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest numpy h5py
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
+    - name: Install package
+      run: |
+        python -m pip install --upgrade-strategy only-if-needed .
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
           pip install --upgrade-strategy only-if-needed "cvxpy<1.4" "scs>=3.0.1,<3.1";
         fi
-    - name: Install package
-      run: |
-        python -m pip install --upgrade-strategy only-if-needed .
     - name: Install Green-MBTools and Test igen
       run: |
         pip install --upgrade-strategy only-if-needed green-mbtools

From 9acd7e28e798dd8aa0d4dfd1c6e4f499a81ada8c Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 17:45:29 -0400
Subject: [PATCH 33/46] remove distutils installation altogether

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 0e37d11..d4e1544 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -30,7 +30,7 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt update
-        sudo apt install python3-distutils libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
+        sudo apt install libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
         sudo apt install build-essential
         python -m pip install --upgrade pip setuptools
         python -m pip install --upgrade pip

From 8a8479f013f3d3b0aa871a844066af9f5237957f Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 18:06:55 -0400
Subject: [PATCH 34/46] remove upgrade strategy things with installation of
 igen

---
 .github/workflows/python-package.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index d4e1544..7ee2805 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -38,10 +38,10 @@ jobs:
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
     - name: Install package
       run: |
-        python -m pip install --upgrade-strategy only-if-needed .
+        python -m pip install .
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
-          pip install --upgrade-strategy only-if-needed "cvxpy<1.4" "scs>=3.0.1,<3.1";
+          pip install "cvxpy<1.4" "scs>=3.0.1,<3.1";
         fi
     - name: Install Green-MBTools and Test igen
       run: |

From 462401e65997493a1b328127f325cd53ac4109c3 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 18:08:55 -0400
Subject: [PATCH 35/46] address library tweaks

---
 .github/workflows/python-package.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 7ee2805..565dbfb 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -39,6 +39,11 @@ jobs:
     - name: Install package
       run: |
         python -m pip install .
+    - name: Tweak library versions
+      run: |
+        if python -c "import sys; exit(sys.version_info >= (3,12))"; then
+          python -m pip install distutils
+        fi
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
           pip install "cvxpy<1.4" "scs>=3.0.1,<3.1";

From 19546eca358d43d171ba3ea7b82aa5186414f7f2 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 19:58:10 -0400
Subject: [PATCH 36/46] distutils still gives an error

---
 .github/workflows/python-package.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 565dbfb..4414ee2 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -41,9 +41,6 @@ jobs:
         python -m pip install .
     - name: Tweak library versions
       run: |
-        if python -c "import sys; exit(sys.version_info >= (3,12))"; then
-          python -m pip install distutils
-        fi
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
           pip install "cvxpy<1.4" "scs>=3.0.1,<3.1";

From e72e703ad8b93444cfc42eeb41efd0adeecb58b2 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Thu, 11 Sep 2025 20:12:20 -0400
Subject: [PATCH 37/46] link quadmath lib

---
 src/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 17df650..7a048c9 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -36,4 +36,4 @@ set_target_properties(pbc0 PROPERTIES
   COMPILE_FLAGS ${OpenMP_C_FLAGS}
   LINK_FLAGS ${OpenMP_C_FLAGS})
 
-target_link_libraries(pbc0 ${BLAS_LIBRARIES} m)
+target_link_libraries(pbc0 ${BLAS_LIBRARIES} m quadmath)

From 75273c7830d3152312100c7a90a2eaecb95f413c Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Fri, 12 Sep 2025 14:56:30 -0400
Subject: [PATCH 38/46] check if scs 3.2.0 fixes error with python 11

---
 .github/workflows/python-package.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 4414ee2..a90f0cb 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -43,7 +43,8 @@ jobs:
       run: |
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
-          pip install "cvxpy<1.4" "scs>=3.0.1,<3.1";
+          pip install "scs==3.2.0";
+          pip install "cvxpy<1.4"
         fi
     - name: Install Green-MBTools and Test igen
       run: |

From c8bf15a020d1cd0bc2cbdcf04f23cefbb6dbb04c Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Fri, 12 Sep 2025 17:09:38 -0400
Subject: [PATCH 39/46] cherry pick scs and cvxpy versions for python 3.11

---
 .github/workflows/python-package.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index a90f0cb..7a059ec 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -32,7 +32,7 @@ jobs:
         sudo apt update
         sudo apt install libblas-dev liblapack-dev libeigen3-dev libgmp-dev libmpfr-dev libfftw3-dev libhdf5-dev
         sudo apt install build-essential
-        python -m pip install --upgrade pip setuptools
+        python -m pip install --upgrade pip setuptools wheel
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest numpy h5py
         pip install --upgrade-strategy only-if-needed ${{ matrix.pyscf-version }}
@@ -43,8 +43,8 @@ jobs:
       run: |
         if [ ${{ matrix.pyscf-version }} = "git+https://github.com/cnyeh/pyscf.git@x2c1e_kpoints" ]; then
           pip install --upgrade "scipy<1.11.0";
-          pip install "scs==3.2.0";
-          pip install "cvxpy<1.4"
+          pip install "scs==3.2.3";
+          pip install "cvxpy==1.4"
         fi
     - name: Install Green-MBTools and Test igen
       run: |

From e35216bec48f9fd11f7226ceedc474cc78251351 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 13 Sep 2025 02:10:20 -0400
Subject: [PATCH 40/46] handle quadmath across platforms

---
 CMakeLists.txt     | 3 +++
 src/CMakeLists.txt | 6 +++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ffaedac..0b9fa72 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -107,6 +107,9 @@ set(MIN_EXPCUTOFF ${libcint_MIN_EXPCUTOFF})
 set(KEEP_GOING ${libcint_KEEP_GOING})
 set(CMAKE_C_CREATE_SHARED_LIBRARY ${libcint_CMAKE_C_CREATE_SHARED_LIBRARY})
 
+check_library_exists(quadmath logq "" HAVE_LIBQUADMATH)
+check_include_file("quadmath.h" HAVE_QUADMATH_H)
+
 add_subdirectory(src)
 add_library(GREEN::IGEN ALIAS pbc0)
 add_dependencies(pbc0 cint)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 7a048c9..2540f56 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -36,4 +36,8 @@ set_target_properties(pbc0 PROPERTIES
   COMPILE_FLAGS ${OpenMP_C_FLAGS}
   LINK_FLAGS ${OpenMP_C_FLAGS})
 
-target_link_libraries(pbc0 ${BLAS_LIBRARIES} m quadmath)
+target_link_libraries(pbc0 ${BLAS_LIBRARIES} m)
+if (HAVE_LIBQUADMATH AND HAVE_QUADMATH_H)
+    target_link_libraries(pbc0 quadmath)
+    target_compile_definitions(pbc0 USE_LIBQUADMATH)
+endif()

From c7ccd4903642cc1797076bc4740b363934866d4c Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 13 Sep 2025 22:40:04 -0400
Subject: [PATCH 41/46] minor fix in cmake

---
 src/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 2540f56..92af259 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -38,6 +38,6 @@ set_target_properties(pbc0 PROPERTIES
 
 target_link_libraries(pbc0 ${BLAS_LIBRARIES} m)
 if (HAVE_LIBQUADMATH AND HAVE_QUADMATH_H)
-    target_link_libraries(pbc0 quadmath)
-    target_compile_definitions(pbc0 USE_LIBQUADMATH)
+    target_link_libraries(pbc0 PUBLIC quadmath)
+    target_compile_definitions(pbc0 PUBLIC USE_LIBQUADMATH)
 endif()

From fcfa630ad08b6ab7ee7fdf2d35429ae2b579dd1d Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Sat, 13 Sep 2025 23:14:30 -0400
Subject: [PATCH 42/46] fix syntax for target_link_libraries

---
 src/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 92af259..3cc36d0 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -36,7 +36,7 @@ set_target_properties(pbc0 PROPERTIES
   COMPILE_FLAGS ${OpenMP_C_FLAGS}
   LINK_FLAGS ${OpenMP_C_FLAGS})
 
-target_link_libraries(pbc0 ${BLAS_LIBRARIES} m)
+target_link_libraries(pbc0 PUBLIC ${BLAS_LIBRARIES} m)
 if (HAVE_LIBQUADMATH AND HAVE_QUADMATH_H)
     target_link_libraries(pbc0 PUBLIC quadmath)
     target_compile_definitions(pbc0 PUBLIC USE_LIBQUADMATH)

From 408a4a72b04da6ce257100dfe56dee21dd9b0ad2 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Mon, 15 Sep 2025 02:37:22 +0530
Subject: [PATCH 43/46] fix assume_a parameter in scipy linalg helper

---
 python/green_igen/linalg_helper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/green_igen/linalg_helper.py b/python/green_igen/linalg_helper.py
index 2784af5..fd7640c 100644
--- a/python/green_igen/linalg_helper.py
+++ b/python/green_igen/linalg_helper.py
@@ -1478,7 +1478,7 @@ def cho_solve(a, b, strict_sym_pos=True):
             on matrix a
     '''
     try:
-        return scipy.linalg.solve(a, b, assume_a=True)
+        return scipy.linalg.solve(a, b, assume_a='pos')
     except numpy.linalg.LinAlgError:
         if strict_sym_pos:
             raise

From b1ef670ab2c42ac06ee2e5af7a269aa83744ee93 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Mon, 15 Sep 2025 02:38:07 +0530
Subject: [PATCH 44/46] update author list email

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6d91c47..48f0eb6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,8 +11,8 @@ cmake.verbose = true
 name = "green-igen"
 version = "0.2.7"
 authors = [
-  { name="Sergei Iskakov", email="siskakov@umich.edu" },
-  { name="Gaurav Harsha" },
+  { name="Sergei Iskakov"},
+  { name="Gaurav Harsha", email="siskakov@umich.edu"},
 ]
 
 dependencies = ["numpy", "h5py", "scipy", "pyscf"]

From 73cdec923b086ae01d7c057138d02cec2f2837c2 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Mon, 15 Sep 2025 02:39:23 +0530
Subject: [PATCH 45/46] cleanup

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 48f0eb6..a95f2cb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,8 +11,8 @@ cmake.verbose = true
 name = "green-igen"
 version = "0.2.7"
 authors = [
-  { name="Sergei Iskakov"},
-  { name="Gaurav Harsha", email="siskakov@umich.edu"},
+  { name="Sergei Iskakov" },
+  { name="Gaurav Harsha", email="siskakov@umich.edu" },
 ]
 
 dependencies = ["numpy", "h5py", "scipy", "pyscf"]

From 8d24eed68559e7436bc48e70af371a52d93abca2 Mon Sep 17 00:00:00 2001
From: Gaurav Harsha <gauravharsha05@gmail.com>
Date: Mon, 15 Sep 2025 16:28:26 +0530
Subject: [PATCH 46/46] fix email id typo

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a95f2cb..1dbc9b2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ name = "green-igen"
 version = "0.2.7"
 authors = [
   { name="Sergei Iskakov" },
-  { name="Gaurav Harsha", email="siskakov@umich.edu" },
+  { name="Gaurav Harsha", email="gharsha@umich.edu" },
 ]
 
 dependencies = ["numpy", "h5py", "scipy", "pyscf"]