From d3c2a17dca9f154518922bb0787e0a3aae6d9ec0 Mon Sep 17 00:00:00 2001 From: sjoudaki Date: Fri, 30 Jan 2026 14:22:55 +0100 Subject: [PATCH 1/5] point towards cloe-org --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 1b7fee55..c3b15f2b 100644 --- a/README.md +++ b/README.md @@ -2,10 +2,10 @@ Logo -[![CI](https://github.com/cloe-euclid/cloe/actions/workflows/ci.yml/badge.svg)](https://github.com/cloe-euclid/cloe/actions/workflows/ci.yml) -[![codecov](https://codecov.io/gh/cloe-euclid/cloe/branch/main/graph/badge.svg?token=6d834ba5-670c-4b8e-af08-12956d5913da)](https://codecov.io/gh/cloe-euclid/cloe) +[![CI](https://github.com/cloe-org/cloe/actions/workflows/ci.yml/badge.svg)](https://github.com/cloe-org/cloe/actions/workflows/ci.yml) +[![codecov](https://codecov.io/gh/cloe-org/cloe/branch/main/graph/badge.svg?token=6d834ba5-670c-4b8e-af08-12956d5913da)](https://codecov.io/gh/cloe-org/cloe) [![License: LGPL-3.0](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.en.html) -[![Documentation](https://readthedocs.org/projects/cloe-euclid/badge/?version=latest)](https://cloe-euclid.readthedocs.io/en/latest/) +[![Documentation](https://readthedocs.org/projects/cloe-org/badge/?version=latest)](https://cloe-org.readthedocs.io/en/latest/) This repository allows the user to obtain model predictions and cosmological parameter constraints for synthetic and real *Euclid* data. It is developed by members of the Euclid Consortium (EC). @@ -24,7 +24,7 @@ It is also possible to analyze the *Euclid* data alongside other external datase [Cobaya](https://cobaya.readthedocs.io/en/latest/) and [CosmoSIS](https://cosmosis.readthedocs.io/en/latest/) platforms. CLOE moreover allows the user to obtain the linear matter power spectrum and background expansion from either of the [CAMB](https://camb.readthedocs.io/en/latest/) and [CLASS](https://lesgourg.github.io/class_public/class.html) Boltzmann codes. -Further documentation is found in the [CLOE Read the Docs](https://cloe-euclid.readthedocs.io/). +Further documentation is found in the [CLOE Read the Docs](https://cloe-org.readthedocs.io/). The full development history is available to EC members [here](https://gitlab.euclid-sgs.uk/pf-ist-likelihood/likelihood-implementation). ## Installation @@ -32,7 +32,7 @@ The full development history is available to EC members [here](https://gitlab.eu Clone the CLOE repository through the following command: ```shell -git clone https://github.com/cloe-euclid/CLOE.git +git clone https://github.com/cloe-org/CLOE.git ``` Next, create a Conda environment using `environment.yml` that we provide, which includes all the required dependencies with fixed versions that have been tested with CLOE: @@ -43,7 +43,7 @@ conda activate cloe pip install . ``` -If our environment does not work on your cluster, we provide additional installation instructions in the [CLOE Read the Docs](https://cloe-euclid.readthedocs.io/). +If our environment does not work on your cluster, we provide additional installation instructions in the [CLOE Read the Docs](https://cloe-org.readthedocs.io/). Lastly, in order to use CLOE with CosmoSIS, one needs to add the line ```shell @@ -108,7 +108,7 @@ Instead of directly editing `config_default.py`, it is also possible to add the These example scripts accomplish exactly the same commands as the `run_cloe.py` instructions. The CLOE team has constructed the scripts from an internal notebook that is based on the contents of `config_default.yaml`. ## Structure of the repository -* **cloe**: folder containing the CLOE source code and unit tests in Python (see the [API documentation](https://cloe-euclid.readthedocs.io/en/latest/api/index.html) for details) +* **cloe**: folder containing the CLOE source code and unit tests in Python (see the [API documentation](https://cloe-org.readthedocs.io/en/latest/api/index.html) for details) * **cosmosis**: folder containing the CLOE source code in Python and configuration files in INI for its CosmoSIS interface * **configs**: folder containing configuration files in YAML, which allow the user to choose analysis settings such as the cosmological probes, summary statistics, scale cuts, parameter space, and systematic uncertainties. * **data**: folder containing the data products (be it real or synthetic) @@ -154,5 +154,5 @@ More broadly, CLOE contains a variety of Jupyter Notebooks in the `notebooks` di ## License and Credits CLOE is released by the Euclid Consortium. It is open source and available under terms consistent with our license based on [LGPL](https://www.gnu.org/licenses/lgpl-3.0). -If you use CLOE, please cite this repository and the CLOE papers (found [here](https://cloe-euclid.readthedocs.io/en/latest/cite_us.html)). +If you use CLOE, please cite this repository and the CLOE papers (found [here](https://cloe-org.readthedocs.io/en/latest/cite_us.html)). In addition, please cite the associated papers and adhere to the corresponding licenses of codes that CLOE utilizes (such as `CAMB`, `CLASS`, `HMCODE`, `BACCO`, and `FAST-PT`). From d56fca73d6e4ddce4fdb997ce59eee5c76dacaf2 Mon Sep 17 00:00:00 2001 From: sjoudaki Date: Fri, 30 Jan 2026 14:43:58 +0100 Subject: [PATCH 2/5] minor tweak --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index c3b15f2b..3c5d8ab5 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![CI](https://github.com/cloe-org/cloe/actions/workflows/ci.yml/badge.svg)](https://github.com/cloe-org/cloe/actions/workflows/ci.yml) [![codecov](https://codecov.io/gh/cloe-org/cloe/branch/main/graph/badge.svg?token=6d834ba5-670c-4b8e-af08-12956d5913da)](https://codecov.io/gh/cloe-org/cloe) [![License: LGPL-3.0](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.en.html) -[![Documentation](https://readthedocs.org/projects/cloe-org/badge/?version=latest)](https://cloe-org.readthedocs.io/en/latest/) +[![Documentation](https://readthedocs.org/projects/cloe-euclid/badge/?version=latest)](https://cloe-euclid.readthedocs.io/en/latest/) This repository allows the user to obtain model predictions and cosmological parameter constraints for synthetic and real *Euclid* data. It is developed by members of the Euclid Consortium (EC). @@ -24,7 +24,7 @@ It is also possible to analyze the *Euclid* data alongside other external datase [Cobaya](https://cobaya.readthedocs.io/en/latest/) and [CosmoSIS](https://cosmosis.readthedocs.io/en/latest/) platforms. CLOE moreover allows the user to obtain the linear matter power spectrum and background expansion from either of the [CAMB](https://camb.readthedocs.io/en/latest/) and [CLASS](https://lesgourg.github.io/class_public/class.html) Boltzmann codes. -Further documentation is found in the [CLOE Read the Docs](https://cloe-org.readthedocs.io/). +Further documentation is found in the [CLOE Read the Docs](https://cloe-euclid.readthedocs.io/). The full development history is available to EC members [here](https://gitlab.euclid-sgs.uk/pf-ist-likelihood/likelihood-implementation). ## Installation @@ -43,7 +43,7 @@ conda activate cloe pip install . ``` -If our environment does not work on your cluster, we provide additional installation instructions in the [CLOE Read the Docs](https://cloe-org.readthedocs.io/). +If our environment does not work on your cluster, we provide additional installation instructions in the [CLOE Read the Docs](https://cloe-euclid.readthedocs.io/). Lastly, in order to use CLOE with CosmoSIS, one needs to add the line ```shell @@ -108,7 +108,7 @@ Instead of directly editing `config_default.py`, it is also possible to add the These example scripts accomplish exactly the same commands as the `run_cloe.py` instructions. The CLOE team has constructed the scripts from an internal notebook that is based on the contents of `config_default.yaml`. ## Structure of the repository -* **cloe**: folder containing the CLOE source code and unit tests in Python (see the [API documentation](https://cloe-org.readthedocs.io/en/latest/api/index.html) for details) +* **cloe**: folder containing the CLOE source code and unit tests in Python (see the [API documentation](https://cloe-euclid.readthedocs.io/en/latest/api/index.html) for details) * **cosmosis**: folder containing the CLOE source code in Python and configuration files in INI for its CosmoSIS interface * **configs**: folder containing configuration files in YAML, which allow the user to choose analysis settings such as the cosmological probes, summary statistics, scale cuts, parameter space, and systematic uncertainties. * **data**: folder containing the data products (be it real or synthetic) @@ -154,5 +154,5 @@ More broadly, CLOE contains a variety of Jupyter Notebooks in the `notebooks` di ## License and Credits CLOE is released by the Euclid Consortium. It is open source and available under terms consistent with our license based on [LGPL](https://www.gnu.org/licenses/lgpl-3.0). -If you use CLOE, please cite this repository and the CLOE papers (found [here](https://cloe-org.readthedocs.io/en/latest/cite_us.html)). +If you use CLOE, please cite this repository and the CLOE papers (found [here](https://cloe-euclid.readthedocs.io/en/latest/cite_us.html)). In addition, please cite the associated papers and adhere to the corresponding licenses of codes that CLOE utilizes (such as `CAMB`, `CLASS`, `HMCODE`, `BACCO`, and `FAST-PT`). From 98aacf28f8bfd09ed2f95376059260fc5a638531 Mon Sep 17 00:00:00 2001 From: sjoudaki Date: Fri, 30 Jan 2026 15:24:40 +0100 Subject: [PATCH 3/5] update ci files --- .github/workflows/build-and-push-image.yml | 2 +- .github/workflows/ci.yml | 4 ++-- README.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build-and-push-image.yml b/.github/workflows/build-and-push-image.yml index 4da1b914..09c94e9c 100644 --- a/.github/workflows/build-and-push-image.yml +++ b/.github/workflows/build-and-push-image.yml @@ -36,4 +36,4 @@ jobs: with: context: . push: true - tags: ghcr.io/cloe-euclid/cloe:${{ env.IMAGE_TAG }} + tags: ghcr.io/cloe-org/cloe:${{ env.IMAGE_TAG }} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bbf5998d..b7294beb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -41,7 +41,7 @@ jobs: - name: Pull image & run tests run: | - IMAGE=ghcr.io/cloe-euclid/cloe:latest + IMAGE=ghcr.io/cloe-org/cloe:latest echo "→ Pulling $IMAGE" docker pull "$IMAGE" @@ -78,7 +78,7 @@ jobs: uses: codecov/codecov-action@v5 with: files: coverage.xml - token: ${{ secrets.CODECOV_TOKEN }} # only needed if your repo is private + token: ${{ secrets.CODECOV_TOKEN_NEW }} # only needed if your repo is private fail_ci_if_error: true - name: Send coverage to Coveralls diff --git a/README.md b/README.md index 3c5d8ab5..455725c6 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ Logo [![CI](https://github.com/cloe-org/cloe/actions/workflows/ci.yml/badge.svg)](https://github.com/cloe-org/cloe/actions/workflows/ci.yml) -[![codecov](https://codecov.io/gh/cloe-org/cloe/branch/main/graph/badge.svg?token=6d834ba5-670c-4b8e-af08-12956d5913da)](https://codecov.io/gh/cloe-org/cloe) +[![codecov](https://codecov.io/gh/cloe-org/cloe/branch/main/graph/badge.svg?token=26c55a1c-87b4-4666-be68-7c3269a5ce86)](https://codecov.io/gh/cloe-org/cloe) [![License: LGPL-3.0](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.en.html) [![Documentation](https://readthedocs.org/projects/cloe-euclid/badge/?version=latest)](https://cloe-euclid.readthedocs.io/en/latest/) From bbcde3a88ab6791856723147c38939222225f4d6 Mon Sep 17 00:00:00 2001 From: sjoudaki Date: Fri, 30 Jan 2026 16:48:22 +0100 Subject: [PATCH 4/5] ci coveralls --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b7294beb..cd42702d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -82,6 +82,7 @@ jobs: fail_ci_if_error: true - name: Send coverage to Coveralls + continue-on-error: true uses: coverallsapp/github-action@v2 env: COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} From 352162fe436ed561c996bbac4210317eaeb6af99 Mon Sep 17 00:00:00 2001 From: sjoudaki Date: Mon, 2 Feb 2026 20:20:00 +0100 Subject: [PATCH 5/5] minor capitalization edit --- docs/source/changelog.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index b4f76d70..ab02e9f8 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -65,7 +65,7 @@ which is when the Euclid Inter-Science Taskforce: Likelihood completed its tenur It includes the FFTLog implementation, a unified treatment of Cobaya and CosmoSIS via the CLOE overlayer, and the ability to read in data files in -the Euclid OU-LE3 format via EuclidLib. This version of CLOE moreover includes an +the Euclid OU-LE3 format via euclidlib. This version of CLOE moreover includes an optimization of the integration strategy for the weak lensing and magnification kernels (resulting in a factor of six speed improvement), along with bug fixes pertaining to the magnification bias, Conda environment, and measurement units.