Adapt links GitLab -> GitHub; Reduce GitLab CI: Only pages with redirect

.gitlab-ci.yml

@@ -1,134 +1,11 @@
-stages:
-  - test
-  - build_doc
-  - publish
-
-default:
-  tags: [k8s]
-
-
 pages:
-  image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-doc/jupyter
+  image: git.physik.uni-wuerzburg.de:25812/z03/pdi/debian:bookworm-buildd
   stage: build_doc
-  rules:
-    - if: '$CI_COMMIT_BRANCH == "master"'
-  tags:
-    - k8s
   script:
-    - git config --global --add safe.directory $PWD
-    - git checkout $CI_COMMIT_BRANCH
-    - pip install --editable .
-    - (cd doc && make)
     - mkdir public
-    - mv doc/_build/html/* public
+    - echo '<meta http-equiv="refresh" content="0; URL=https://alf.physik.uni-wuerzburg.de/pyalf-doc" />' > public/index.html
   artifacts:
     paths:
       - public
-
-
-check_docstrings:
-  stage: test
-  allow_failure: true
-  image: python:alpine
-  rules:
-    - changes:
-      - py_alf
-      - .gitlab-ci.yml
-  script:
-    - pip install ruff
-    - ruff check --select D
-
-
-build_test:
-  stage: publish
-  image: ghcr.io/astral-sh/uv:alpine
-  rules:
-    - if: '$CI_COMMIT_BRANCH != "master"'
-  script:
-    - apk add git
-    - uv build
-
-
-build:
-  stage: publish
-  image: ghcr.io/astral-sh/uv:alpine
   rules:
     - if: '$CI_COMMIT_BRANCH == "master"'
-  script:
-    - apk add git
-    - uv build
-    - uv publish --username $TWINE_USERNAME --password $TWINE_PASSWORD
-
-
-test:
-  stage: test
-  image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/$IMAGE_MINOR
-  rules:
-    - changes:
-      - py_alf
-      - tests
-      - .gitlab-ci.yml
-  parallel:
-    matrix:
-      - MACHINE: GNU
-        IMAGE_MINOR: [bullseye, bookworm, trixie, tumbleweed]
-  script:
-    - pip install pylint ruff pytest
-    - pylint -E py_alf/
-    - ruff check --exclude doc
-    - pip install .
-    - pytest
-    - alf_run --machine $MACHINE --sims_file py_alf/cli/Sims
-
-
-exec_notebook:
-  stage: test
-  image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/$IMAGE_MINOR
-  rules:
-    - changes:
-      - Notebooks/*
-  parallel:
-    matrix:
-      - MACHINE: GNU
-        IMAGE_MINOR: [bullseye, bookworm, trixie, tumbleweed]
-        NOTEBOOK: 
-          - parallel_tempering.ipynb
-          - projective_algorithm.ipynb
-          - pyALF_new_features.ipynb
-          - testing_against_ED.ipynb
-          - trotter_error.ipynb
-          - tV_model.ipynb
-  script:
-    - pip install jupyter nbconvert .
-    - cd Notebooks/
-    - jupyter-nbconvert --execute --inplace $NOTEBOOK
-
-
-warn_pylint:
-  stage: test
-  image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/$IMAGE_MINOR
-  rules:
-    - changes:
-      - py_alf
-      - .gitlab-ci.yml
-  parallel:
-    matrix:
-      - IMAGE_MINOR: [bullseye, bookworm, trixie, tumbleweed]
-  allow_failure: true
-  script:
-    - pip install pylint
-    - pylint py_alf/
-
-warn_ruff:
-  stage: test
-  image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/$IMAGE_MINOR
-  rules:
-    - changes:
-      - py_alf
-      - .gitlab-ci.yml
-  parallel:
-    matrix:
-      - IMAGE_MINOR: [bullseye, bookworm, trixie, tumbleweed]
-  script:
-    - pip install ruff
-    - ruff check --exclude doc

Notebooks/minimal_ALF_run.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this bare-bones example we use the [pyALF](https://git.physik.uni-wuerzburg.de/ALF/pyALF/-/tree/master/) interface to run the canonical Hubbard model on a default configuration: a $6\\times6$ square grid, with interaction strength $U=4$ and inverse temperature $\\beta = 5$.  \n",
+    "In this bare-bones example we use the [pyALF](https://github.com/ALF-QMC/pyALF) interface to run the canonical Hubbard model on a default configuration: a $6\\times6$ square grid, with interaction strength $U=4$ and inverse temperature $\\beta = 5$.  \n",
     "\n",
     "Bellow we go through the steps for performing the simulation and outputting observables.\n",
     "\n",
@@ -33,7 +33,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**2.** Create an instance of `ALF_source`, downloading the ALF source code from the [ALF repository](https://git.physik.uni-wuerzburg.de/ALF/ALF/-/tree/master/), if `alf_dir` does not exist. Gets alf_dir from environment variable `$ALF_DIR`, or defaults to \"./ALF\", if not present:"
+    "**2.** Create an instance of `ALF_source`, downloading the ALF source code from the [ALF repository](https://github.com/ALF-QMC/ALF/-/tree/master/), if `alf_dir` does not exist. Gets alf_dir from environment variable `$ALF_DIR`, or defaults to \"./ALF\", if not present:"
    ]
   },
   {

Notebooks/parallel_tempering.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "ALF is compiled from source, which is downloaded from the [ALF repository](https://git.physik.uni-wuerzburg.de/ALF/ALF) when not found locally."
+    "ALF is compiled from source, which is downloaded from the [ALF repository](https://github.com/ALF-QMC/ALF) when not found locally."
    ]
   },
   {

Notebooks/projective_algorithm.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this example we use the [pyALF](https://git.physik.uni-wuerzburg.de/ALF/pyALF/-/tree/master/) interface to run ALF's projective algorithm with the Mz choice of Hubbard Stratonovich transformation on a 4-site ring.\n",
+    "In this example we use the [pyALF](https://github.com/ALF-QMC/pyALF) interface to run ALF's projective algorithm with the Mz choice of Hubbard Stratonovich transformation on a 4-site ring.\n",
     "\n",
     "The projective approach is the method of choice if  one is interested in ground-state properties. The starting point is a pair of trial wave functions,  $|\\Psi_{T,L/R} \\rangle$,  that are  not orthogonal to the ground state $|\\Psi_0 \\rangle$:\n",
     "$$\n",
@@ -23,7 +23,7 @@
     "\t \\frac{ \\langle \\Psi_{T,L} | e^{-\\theta \\hat{H}}  e^{-(\\beta - \\tau)\\hat{H}  }\\hat{O} e^{- \\tau  \\hat{H} }   e^{-\\theta \\hat{H}} | \\Psi_{T,R} \\rangle } \n",
     "\t        { \\langle \\Psi_{T,L} | e^{-(2 \\theta + \\beta) \\hat{H}  } | \\Psi_{T,R} \\rangle } ,\n",
     "$$\n",
-    "where $\\beta$ defines the imaginary time range where observables (time displaced and equal time) are measured and $\\tau$ varies from $0$ to $\\beta$ in the calculation of time-displace observables. For further details, see Sec. 3 of [ALF documentation](https://git.physik.uni-wuerzburg.de/ALF/ALF/-/blob/master/Documentation/doc.pdf).\n",
+    "where $\\beta$ defines the imaginary time range where observables (time displaced and equal time) are measured and $\\tau$ varies from $0$ to $\\beta$ in the calculation of time-displace observables. For further details, see Sec. 3 of [ALF documentation](https://alf.physik.uni-wuerzburg.de/doc.pdf).\n",
     "\n",
     "---\n",
     "\n",

Notebooks/pyALF_new_features.ipynb

@@ -87,7 +87,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**3.** Compile ALF, downloading it first from the [ALF repository](https://git.physik.uni-wuerzburg.de/ALF/ALF/-/tree/master/) if not found locally. This may take a few minutes:"
+    "**3.** Compile ALF, downloading it first from the [ALF repository](https://github.com/ALF-QMC/ALF/-/tree/master/) if not found locally. This may take a few minutes:"
    ]
   },
   {

Notebooks/tV_model.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this example we use the [pyALF](https://git.physik.uni-wuerzburg.de/ALF/pyALF/-/tree/master/) interface to run the one dimensional t-V model of spinless fermions, given by:\n",
+    "In this example we use the [pyALF](https://github.com/ALF-QMC/pyALF) interface to run the one dimensional t-V model of spinless fermions, given by:\n",
     "$$\n",
     "\\hat{H} =  -t \\sum_{i} \\left( \\hat{c}^{\\dagger}_{i}  \\hat{c}^{\\phantom\\dagger}_{i+a}      + \\hat{c}^{\\dagger}_{i+a}  \\hat{c}^{\\phantom\\dagger}_{i} \\right) - V \\sum_{i}  \\left( \\hat{c}^{\\dagger}_{i}  \\hat{c}^{\\phantom\\dagger}_{i+a}      + \\hat{c}^{\\dagger}_{i+a}  \\hat{c}^{\\phantom\\dagger}_{i} \\right)^2.\n",
     "$$\n",
@@ -67,7 +67,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**3.** Compile ALF, downloading it first from the [ALF repository](https://git.physik.uni-wuerzburg.de/ALF/ALF/-/tree/master/) if not found locally. This may take a few minutes:"
+    "**3.** Compile ALF, downloading it first from the [ALF repository](https://github.com/ALF-QMC/ALF/-/tree/master/) if not found locally. This may take a few minutes:"
    ]
   },
   {

Notebooks/testing_against_ED.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this example we use the [pyALF](https://git.physik.uni-wuerzburg.de/ALF/pyALF/-/tree/master/) interface to run ALF with the Mz choice of Hubbard Stratonovitch  transformation on a four site ring, at $U/t=4$  and inverse temperature $\\beta t = 2$.  For this set of parameters, the exact  internal energy reads:   \n",
+    "In this example we use the [pyALF](https://github.com/ALF-QMC/pyALF) interface to run ALF with the Mz choice of Hubbard Stratonovitch  transformation on a four site ring, at $U/t=4$  and inverse temperature $\\beta t = 2$.  For this set of parameters, the exact  internal energy reads:   \n",
     "$$\n",
     " \\left\\langle -t \\sum_{\\langle i,j\\rangle, \\sigma} \\hat{c}_{i,\\sigma}^{\\dagger} \\hat{c}_{j,\\sigma}^{\\phantom\\dagger}   +  U  \\sum_{i=1}^{N} \\hat{n}_{i,\\uparrow}\\hat{n}_{j,\\downarrow}  \\right\\rangle  =   -1.47261997 t \n",
     "$$\n",

Notebooks/trotter_error.ipynb

@@ -11,15 +11,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this example we use the [pyALF](https://git.physik.uni-wuerzburg.de/ALF/pyALF/-/tree/master/) interface to run ALF with the Mz choice of Hubbard-Stratonovich transformation (i.e., coupled to the $z$-component of the spin) on a $6\\times 6$ site square lattice, at $U/t=4$ half-band filling, and inverse temperature $\\beta t = 5$.\n",
+    "In this example we use the [pyALF](https://github.com/ALF-QMC/pyALF) interface to run ALF with the Mz choice of Hubbard-Stratonovich transformation (i.e., coupled to the $z$-component of the spin) on a $6\\times 6$ site square lattice, at $U/t=4$ half-band filling, and inverse temperature $\\beta t = 5$.\n",
     "\n",
     "We carry out a systematic $\\Delta \\tau  t$ extrapolation keeping    $\\Delta \\tau t  L_\\text{Trotter} = 2$  constant. Recall that  the formulation of the auxiliary field QMC approach is based on the symmetric Trotter decomposition \n",
     "$$\n",
     "e^{ -\\Delta \\tau \\left( \\hat{A} + \\hat{B} \\right) }  =  e^{ -\\Delta \\tau \\hat{A}/2}  e^{ -\\Delta \\tau  \\hat{B}  }   e^{ -\\Delta \\tau \\hat{A}/2}  +  \\mathcal{O} \\left (\\Delta  \\tau^3\\right)\n",
     "$$\n",
     "The overall error produced by this approximation is of the order $\\Delta \\tau^2$.  \n",
     "\n",
-    "Bellow we go through the steps for performing this extrapolation: setting the simulation parameters, running it and analysing the data. A reference plot for this analyses is found in [ALF documentation](https://git.physik.uni-wuerzburg.de/ALF/ALF/-/blob/master/Documentation/doc.pdf), Sec. 2.3.2 (Symmetric Trotter decomposition).\n",
+    "Bellow we go through the steps for performing this extrapolation: setting the simulation parameters, running it and analysing the data. A reference plot for this analyses is found in [ALF documentation](https://alf.physik.uni-wuerzburg.de/doc.pdf), Sec. 2.3.2 (Symmetric Trotter decomposition).\n",
     "\n",
     "---\n",
     "\n",
@@ -377,8 +377,13 @@
    "source": [
     "---\n",
     "## Exercises\n",
-    "1. Try out the four different combinations for `Checkerboard` and `Symm` settings in order to observe their effect on the output and run time. Reference: Sec. 2.3.2 - Symmetric Trotter decomposition - of the [ALF documentation](https://git.physik.uni-wuerzburg.de/ALF/ALF/-/blob/master/Documentation/doc.pdf), especially Fig. 2."
+    "1. Try out the four different combinations for `Checkerboard` and `Symm` settings in order to observe their effect on the output and run time. Reference: Sec. 2.3.2 - Symmetric Trotter decomposition - of the [ALF documentation](https://alf.physik.uni-wuerzburg.de/doc.pdf)), especially Fig. 2."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

README.md

@@ -3,7 +3,7 @@
 
 ## pyALF
 
-A Python package building on top of [ALF](https://git.physik.uni-wuerzburg.de/ALF/ALF), meant to simplify the different steps of working with ALF, including:
+A Python package building on top of [ALF](https://github.com/ALF-QMC/ALF), meant to simplify the different steps of working with ALF, including:
 
 * Obtaining and compiling the ALF source code
 * Preparing and running simulations
@@ -35,7 +35,7 @@ pyALF can be installed via the Python package installer [pip](https://pip.pypa.i
 pip install pyALF
 ```
 
-For running ALF, you will additionaly need the [ALF prerequsites](https://git.physik.uni-wuerzburg.de/ALF/ALF#prerequisites).
+For running ALF, you will additionaly need the [ALF prerequsites](https://github.com/ALF-QMC/ALF#prerequisites).
 
 Alternatively, one could use [this Docker image](https://hub.docker.com/r/alfcollaboration/jupyter-pyalf-full), which has ALF, pyALF and a Jupyter server pre-installed.
 
@@ -51,7 +51,7 @@ or a
 The following example shows how to install pyALF in development mode using venv.
 
 ```bash
-git clone https://git.physik.uni-wuerzburg.de/ALF/pyALF.git
+git clone https://github.com/ALF-QMC/pyALF.git
 cd pyALF
 python -m venv .venv
 source .venv/bin/activate

doc/_templates/sidebar_pdf_commit_.html

@@ -1,6 +1,6 @@
 <ul class="navbar-icon-links navbar-nav" aria-label="Icon Links">
   <li class="nav-item">
-    <a href="/Jonas_schwab/pyalf-docu/doc.pdf" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom" aria-label="Download PDF" data-bs-original-title="Download PDF">
+    <a href="https://alf.physik.uni-wuerzburg.de/pyalf-doc/doc.pdf" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom" aria-label="Download PDF" data-bs-original-title="Download PDF">
       <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="96" height="20" role="img" aria-label="Download: PDF">
         <title>Download PDF</title>
         <linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/>

doc/source/examples/Nematic_example_1.ipynb

@@ -52,7 +52,7 @@
    },
    "source": [
     "## ALF_source\n",
-    "Create instance of `ALF_source`, then we download the `Nematic_Dirac` Hamiltonian from the [Hamiltonian repository](https://git.physik.uni-wuerzburg.de/ALF/hamiltonians/).\n",
+    "Create instance of `ALF_source`, then we download the `Nematic_Dirac` Hamiltonian from the [Hamiltonian repository](https://github.com/ALF-QMC/Hamiltonians/).\n",
     "\n",
     "Reminder: Directory containing the ALF code is taken from environment variable `$ALF_DIR`, if present."
    ]
@@ -81,7 +81,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "78cd3fec-dfec-41e6-90b4-5674baf77513",
    "metadata": {
     "editable": true,
@@ -112,7 +112,7 @@
    "source": [
     "ham_name = \"Nematic_Dirac\"\n",
     "urlretrieve(\n",
-    "    f'https://git.physik.uni-wuerzburg.de/ALF/hamiltonians/-/raw/main/Hamiltonians/{ham_name}/Hamiltonian_{ham_name}_smod.F90',\n",
+    "    f'https://raw.githubusercontent.com/ALF-QMC/Hamiltonians/refs/heads/main/Hamiltonians/{ham_name}/Hamiltonian_{ham_name}_smod.F90',\n",
     "    os.path.join(alf_src.alf_dir, \"Prog\", \"Hamiltonians\", f\"Hamiltonian_{ham_name}_smod.F90\")\n",
     ")"
    ]

doc/source/front.md

@@ -8,7 +8,7 @@ Aiming to address this challenge, pyALF is a set of Python scripts built on top
 - Preparing and running simulations
 - Postprocessing and displaying the data obtained during the simulation 
 
-The source codes for both ALF and pyALF are publicly available at [https://git.physik.uni-wuerzburg.de/ALF](https://git.physik.uni-wuerzburg.de/ALF).
+The source codes for both ALF and pyALF are publicly available at [https://github.com/ALF-QMC](https://github.com/ALF-QMC).
 
 This documentation is structured in the following way: