From 1d323b5dd3eb4ef5a9a86f9c27d7acf2107a1f72 Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 14:50:57 +0000 Subject: [PATCH 01/10] Edit README.md --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 8bf09f9..4a7672f 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,10 @@ # Foccus Project -Foccus is a general-purpose project repository template. It provides a clean and organized starting point for software development, data science, machine learning, or research projects. +[![GitLab pipeline status](https://gitlab.com/your-namespace/foccus/badges/main/pipeline.svg)](https://gitlab.com/your-namespace/foccus/pipelines) +![License](https://img.shields.io/badge/license-MIT-blue.svg) +![Python](https://img.shields.io/badge/python-3.8%2B-blue) + +**Foccus** is a versatile and scalable template for structuring software, data science, and machine learning projects. Whether you're conducting research or building a production system, Foccus helps maintain clarity, reproducibility, and modularity across the development lifecycle. ## Project Structure -- GitLab From 660b16a029f4fc0f68adb2ac2dd3c5ba873b98f0 Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 14:51:56 +0000 Subject: [PATCH 02/10] Edit README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4a7672f..ac63245 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Foccus Project -[![GitLab pipeline status](https://gitlab.com/your-namespace/foccus/badges/main/pipeline.svg)](https://gitlab.com/your-namespace/foccus/pipelines) +[![GitLab pipeline status](https://gitlab.com/socib/foccus/badges/main/pipeline.svg)](https://gitlab.com/your-namespace/foccus/pipelines) ![License](https://img.shields.io/badge/license-MIT-blue.svg) ![Python](https://img.shields.io/badge/python-3.8%2B-blue) -- GitLab From 1c8f95cae11a147c149e9be5d9bb340c66a0662f Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 14:52:43 +0000 Subject: [PATCH 03/10] Edit README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ac63245..1c7de7b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Foccus Project -[![GitLab pipeline status](https://gitlab.com/socib/foccus/badges/main/pipeline.svg)](https://gitlab.com/your-namespace/foccus/pipelines) +[![GitLab pipeline status](https://gitlab.com/socib/foccus/badges/main/pipeline.svg)](https://gitlab.com/socib/foccus/pipelines) ![License](https://img.shields.io/badge/license-MIT-blue.svg) ![Python](https://img.shields.io/badge/python-3.8%2B-blue) -- GitLab From 748438d44df4665b26238cb1df0afdc27c1233f0 Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 15:04:48 +0000 Subject: [PATCH 04/10] Edit .gitlab-ci.yml --- .gitlab-ci.yml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 97b1a10..5af2fa9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -2,7 +2,11 @@ stages: - test -test: - script: +run-tests: + stage: test + image: python:3.10 + before_script: - pip install -r requirements.txt - - pytest + - pip install pytest + script: + - pytest \ No newline at end of file -- GitLab From 83af1294f500f35ae7991021f73aa79cd5a6d7d9 Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 15:10:36 +0000 Subject: [PATCH 05/10] Edit README.md --- README.md | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 1c7de7b..22e1b27 100644 --- a/README.md +++ b/README.md @@ -10,24 +10,25 @@ ``` foccus/ -├── README.md # Project overview, usage instructions -├── LICENSE # License file -├── .gitignore # Files to ignore in Git -├── .gitlab-ci.yml # CI/CD pipeline definition -├── docs/ # Documentation -├── src/ # Source code -├── tests/ # Unit and integration tests -├── data/ # Data files -│ └── raw/ # Raw data -├── notebooks/ # Jupyter notebooks for exploration -├── scripts/ # Automation and deployment scripts -├── figure/ # Figures, plots, and graphics +├── README.md # Project overview, usage instructions +├── LICENSE # License file +├── .gitignore # Files to ignore in Git +├── .gitlab-ci.yml # CI/CD pipeline definition +├── docs/ # Documentation +├── src/ # Source code +├── tests/ # Unit and integration tests +├── data/ # Data files +│ └── Observations/ # SLA data +│ └── Oceanic_models/ # Models data +├── notebooks/ # Jupyter notebooks for exploration +├── scripts/ # Automation and deployment scripts +├── figure/ # Figures, plots, and graphics ``` ## Getting Started ### Prerequisites -- Python 3.x +- Python 3.8 o superior - Git ### Setup -- GitLab From 1d8a38c13408e0c699eb603f971d83913bea5f3d Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 15:17:04 +0000 Subject: [PATCH 06/10] Edit README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 22e1b27..3ed22f1 100644 --- a/README.md +++ b/README.md @@ -41,8 +41,8 @@ cd foccus 2. Create and activate virtual environment (optional but recommended): ```bash -python -m venv .venv -source .venv/bin/activate # On Windows: .venv\Scripts\activate +conda env create -f environment.yml +conda activate foccus-env ``` 3. Install dependencies: -- GitLab From c359d2a725c8d164edebe1426445b69252f7e785 Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 15:18:45 +0000 Subject: [PATCH 07/10] Edit .gitlab-ci.yml --- .gitlab-ci.yml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 5af2fa9..daee8a8 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,12 +1,17 @@ # CI/CD Pipeline (adjust according to your needs) +image: python:3.10 + stages: - test -run-tests: +before_script: + - python -m venv venv + - source venv/bin/activate + - pip install --upgrade pip + - pip install -r requirements.txt + - pip install pytest + +test: stage: test - image: python:3.10 - before_script: - - pip install -r requirements.txt - - pip install pytest script: - - pytest \ No newline at end of file + - pytest -- GitLab From 4dcacc17f3f640616e25da0ecb7e1b361adfb2ab Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 15:22:37 +0000 Subject: [PATCH 08/10] Edit README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 3ed22f1..62be0f8 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,7 @@ foccus/ ### Prerequisites - Python 3.8 o superior +- [Conda](https://docs.conda.io/en/latest/miniconda.html) (Miniconda o Anaconda) - Git ### Setup -- GitLab From e7ea3758224ca25db5b44fe894db473a0467ad2a Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Thu, 26 Jun 2025 15:25:48 +0000 Subject: [PATCH 09/10] Edit README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 62be0f8..b3607c9 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,8 @@ foccus/ ├── LICENSE # License file ├── .gitignore # Files to ignore in Git ├── .gitlab-ci.yml # CI/CD pipeline definition +├── requirements.txt # Python dependencies (pip) +├── environment.yml # Conda environment specification ├── docs/ # Documentation ├── src/ # Source code ├── tests/ # Unit and integration tests -- GitLab From 3c00785a3ee5494cebd8ccef3484e7a6648e787d Mon Sep 17 00:00:00 2001 From: Maximo Garcia-Jove Navarro Date: Fri, 27 Jun 2025 10:17:50 +0000 Subject: [PATCH 10/10] Edit .gitlab-ci.yml --- .gitlab-ci.yml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index daee8a8..3a0af67 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,17 +1,19 @@ # CI/CD Pipeline (adjust according to your needs) -image: python:3.10 +image: mambaorg/micromamba:1.4.2 stages: - test -before_script: - - python -m venv venv - - source venv/bin/activate - - pip install --upgrade pip - - pip install -r requirements.txt - - pip install pytest +variables: + MAMBA_DOCKERFILE_ACTIVATE: 1 + MAMBA_ROOT_PREFIX: /opt/conda + ENV_NAME: foccus-env test: stage: test script: - - pytest + - micromamba create -y -n $ENV_NAME -f environment.yml + - micromamba run -n $ENV_NAME which python + - micromamba run -n $ENV_NAME python --version + - micromamba run -n $ENV_NAME pip install pytest + - micromamba run -n $ENV_NAME pytest tests/ -- GitLab