From 578599a64039d95870a9e7ad0042b00e3ace0743 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 17:23:26 +0100
Subject: [PATCH 01/23] attempt to fix api ref in redthedoc

---
 .readthedocs.yaml     | 6 +++++-
 docs/index.md         | 4 +++-
 docs/requirements.txt | 7 -------
 3 files changed, 8 insertions(+), 9 deletions(-)
 delete mode 100644 docs/requirements.txt

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index ff7f01ab..c317c145 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -5,8 +5,12 @@
 # Required
 version: 2
 python:
+  version: 3.8
   install:
-    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
 
 # Set the OS, Python version and other tools you might need
 build:
diff --git a/docs/index.md b/docs/index.md
index 163cc7a4..de7135a5 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -86,9 +86,11 @@ user/metadata
 
 dev/contribute
 dev/buildDoc
+api/modules
 ```
 
-# API Reference
+
+# Indices and tables
 [//]: # (- {ref}`ppanggolin package`)
 
 - {ref}`genindex`
diff --git a/docs/requirements.txt b/docs/requirements.txt
deleted file mode 100644
index 87dbffaa..00000000
--- a/docs/requirements.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-sphinx==6.2.1
-sphinx_rtd_theme==1.2.2
-readthedocs-sphinx-search==0.3.1
-sphinx-autobuild==2021.3.14
-myst-parser==1.0.0
-docutils==0.18.1
-sphinxcontrib.mermaid==0.9.2
\ No newline at end of file

From 354d8197788aa9bda535540d671270361e1d29c7 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 17:25:42 +0100
Subject: [PATCH 02/23] fix python version

---
 .readthedocs.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index c317c145..aa426ef1 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -5,7 +5,6 @@
 # Required
 version: 2
 python:
-  version: 3.8
   install:
     - method: pip
       path: .

From efcd3e4e6d5abe139660a5a5781d296b027c5826 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 17:33:26 +0100
Subject: [PATCH 03/23] attempt to install doc dep with pip doc

---
 .readthedocs.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index aa426ef1..6b3085f5 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -7,9 +7,7 @@ version: 2
 python:
   install:
     - method: pip
-      path: .
-      extra_requirements:
-        - docs
+      path: .[doc]
 
 # Set the OS, Python version and other tools you might need
 build:

From 598d33e98fd0a8cada37ff2036ab79d15c530981 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 17:45:09 +0100
Subject: [PATCH 04/23] add requirements of all python depencies in the toml

---
 pyproject.toml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 67b67f1b..da928ce3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,18 @@
 requires = [
     "setuptools",
     "setuptools-scm",
-    "cython"
+    "cython",
+    tqdm>=4.64,
+    tables>=3.7,
+    pyrodigal>=3.0.1,
+    networkx>=3.0,
+    scipy>=1.10.0,
+    plotly>=4.14.3,
+    gmpy2>=2.1.2,
+    pandas>=2.0,
+    colorlover>=0.3,
+    numpy>=1.24,
+    bokeh>=2.4.2,<3,
 ]
 build-backend = "setuptools.build_meta"
 py_modules=["ppanggolin"]

From 9ec3df0d8c893c235bd1d098838801bc980b7f85 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 17:55:59 +0100
Subject: [PATCH 05/23] add all python dependencies in toml

---
 pyproject.toml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index da928ce3..0592ea46 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,17 +3,17 @@ requires = [
     "setuptools",
     "setuptools-scm",
     "cython",
-    tqdm>=4.64,
-    tables>=3.7,
-    pyrodigal>=3.0.1,
-    networkx>=3.0,
-    scipy>=1.10.0,
-    plotly>=4.14.3,
-    gmpy2>=2.1.2,
-    pandas>=2.0,
-    colorlover>=0.3,
-    numpy>=1.24,
-    bokeh>=2.4.2,<3,
+    "tqdm>=4.64",
+    "tables>=3.7",
+    "pyrodigal>=3.0.1",
+    "networkx>=3.0",
+    "scipy>=1.10.0",
+    "plotly>=4.14.3",
+    "gmpy2>=2.1.2",
+    "pandas>=2.0",
+    "colorlover>=0.3",
+    "numpy>=1.24",
+    "bokeh>=2.4.2,<3"
 ]
 build-backend = "setuptools.build_meta"
 py_modules=["ppanggolin"]

From efe18b5da2e203ce5b1deb69afa1c6575b8d0fc6 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 18:26:00 +0100
Subject: [PATCH 06/23] try install in readthedoc with conda

---
 .readthedocs.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 6b3085f5..6b22a90e 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -14,11 +14,12 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.8"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
+    python: "mambaforge-22.9"
 
+conda:
+  environment: ppanggolin_env.yaml
+
+  
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
    configuration: docs/conf.py

From 6584f9e5fc2daa43a2a8cda77450e15f0054cb78 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 18:32:26 +0100
Subject: [PATCH 07/23] try without the build lines

---
 .readthedocs.yaml | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 6b22a90e..cbb0f0c5 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -7,17 +7,19 @@ version: 2
 python:
   install:
     - method: pip
-      path: .[doc]
+      path: .
+      extra_requirements:
+        - doc
 
 # Set the OS, Python version and other tools you might need
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.8"
-    python: "mambaforge-22.9"
+# build:
+#   os: ubuntu-22.04
+#   tools:
+#     python: "3.8"
+#     python: "mambaforge-22.9"
 
-conda:
-  environment: ppanggolin_env.yaml
+# conda:
+#   environment: ppanggolin_env.yaml
 
   
 # Build documentation in the "docs/" directory with Sphinx

From a6d15dfaab646c5edfe9551e73d0b4a5a0f69ebf Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 18:36:09 +0100
Subject: [PATCH 08/23] update .readthedocs.yaml

---
 .readthedocs.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index cbb0f0c5..a0eee30a 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -12,9 +12,9 @@ python:
         - doc
 
 # Set the OS, Python version and other tools you might need
-# build:
-#   os: ubuntu-22.04
-#   tools:
+build:
+  os: ubuntu-22.04
+  tools:
 #     python: "3.8"
 #     python: "mambaforge-22.9"
 

From 2782c16f8e4c891a1533d49fc74f50d34edbd23d Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 18:37:09 +0100
Subject: [PATCH 09/23] update .readthedocs.yaml

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index a0eee30a..e6938f57 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -15,7 +15,7 @@ python:
 build:
   os: ubuntu-22.04
   tools:
-#     python: "3.8"
+     python: "3.8"
 #     python: "mambaforge-22.9"
 
 # conda:

From 7c6a178f621fc44a8fbc401e9dd7d06257be15c1 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 19:13:48 +0100
Subject: [PATCH 10/23] update .readthedocs.yaml

---
 .readthedocs.yaml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index e6938f57..a5e8b2ca 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -4,18 +4,20 @@
 
 # Required
 version: 2
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc
+# python:
+#   install:
+#     - method: pip
+#       path: .
+#       extra_requirements:
+#         - doc
 
 # Set the OS, Python version and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
-     python: "3.8"
+    python: "3.8"
+  commands:
+    - pip install .[doc]
 #     python: "mambaforge-22.9"
 
 # conda:

From cf2598669487521d5b65cbbfe17da4248c7f75e3 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 19:21:21 +0100
Subject: [PATCH 11/23] update .readthedocs.yaml

---
 .readthedocs.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index a5e8b2ca..12fcc0ac 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -4,12 +4,12 @@
 
 # Required
 version: 2
-# python:
-#   install:
-#     - method: pip
-#       path: .
-#       extra_requirements:
-#         - doc
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
 
 # Set the OS, Python version and other tools you might need
 build:

From d0cf4dfac555bc74e5fd6d4097e1ef9c39e0a154 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Mon, 18 Dec 2023 19:32:21 +0100
Subject: [PATCH 12/23] update .readthedocs.yaml

---
 .readthedocs.yaml |  2 --
 pyproject.toml    | 13 ++++++++++++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 12fcc0ac..a69299f1 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -16,8 +16,6 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.8"
-  commands:
-    - pip install .[doc]
 #     python: "mambaforge-22.9"
 
 # conda:
diff --git a/pyproject.toml b/pyproject.toml
index 0592ea46..b0f6aa15 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,7 +56,18 @@ doc = [
     "sphinx-autobuild==2021.3.14",
     "myst-parser==2",
     "docutils==0.18.1",
-    "sphinxcontrib.mermaid==0.9.2"
+    "sphinxcontrib.mermaid==0.9.2",
+    "tqdm>=4.64",
+    "tables>=3.7",
+    "pyrodigal>=3.0.1",
+    "networkx>=3.0",
+    "scipy>=1.10.0",
+    "plotly>=4.14.3",
+    "gmpy2>=2.1.2",
+    "pandas>=2.0",
+    "colorlover>=0.3",
+    "numpy>=1.24",
+    "bokeh>=2.4.2,<3"
 ]
 test = [
     "pytest>=7.0.0"

From e167acec37774879214334389a7b5e968476cd50 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 09:24:49 +0100
Subject: [PATCH 13/23] add modules md entry point of api ref

---
 docs/api/modules.md | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 docs/api/modules.md

diff --git a/docs/api/modules.md b/docs/api/modules.md
new file mode 100644
index 00000000..5ba103b1
--- /dev/null
+++ b/docs/api/modules.md
@@ -0,0 +1,18 @@
+# ppanggolin
+
+
+
+
+```{toctree}
+:maxdepth: 2
+
+ppanggolin
+```
+
+
+# Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
+

From 42fc5e3cad6b59c7094c76bbe582fdda60463654 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 09:36:40 +0100
Subject: [PATCH 14/23] add API ref in toctree

---
 docs/api/indice_and_table.md |  7 +++++++
 docs/api/modules.md          | 14 ++------------
 2 files changed, 9 insertions(+), 12 deletions(-)
 create mode 100644 docs/api/indice_and_table.md

diff --git a/docs/api/indice_and_table.md b/docs/api/indice_and_table.md
new file mode 100644
index 00000000..d8eafa38
--- /dev/null
+++ b/docs/api/indice_and_table.md
@@ -0,0 +1,7 @@
+# Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
+
+
diff --git a/docs/api/modules.md b/docs/api/modules.md
index 5ba103b1..6e569604 100644
--- a/docs/api/modules.md
+++ b/docs/api/modules.md
@@ -1,18 +1,8 @@
-# ppanggolin
-
-
-
+# API Reference
 
 ```{toctree}
 :maxdepth: 2
-
 ppanggolin
+indice_and_table
 ```
 
-
-# Indices and tables
-
-- {ref}`genindex`
-- {ref}`modindex`
-- {ref}`search`
-

From 3227875e7b8709f8f2b4342a370c714d83eed6e2 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 10:05:12 +0100
Subject: [PATCH 15/23] add new cat in toml to improve install in readthedoc

---
 .readthedocs.yaml |  1 +
 pyproject.toml    | 21 ++++++---------------
 2 files changed, 7 insertions(+), 15 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index a69299f1..92e946c5 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -10,6 +10,7 @@ python:
       path: .
       extra_requirements:
         - doc
+        - python_deps
 
 # Set the OS, Python version and other tools you might need
 build:
diff --git a/pyproject.toml b/pyproject.toml
index b0f6aa15..3bfbbe77 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,18 +2,7 @@
 requires = [
     "setuptools",
     "setuptools-scm",
-    "cython",
-    "tqdm>=4.64",
-    "tables>=3.7",
-    "pyrodigal>=3.0.1",
-    "networkx>=3.0",
-    "scipy>=1.10.0",
-    "plotly>=4.14.3",
-    "gmpy2>=2.1.2",
-    "pandas>=2.0",
-    "colorlover>=0.3",
-    "numpy>=1.24",
-    "bokeh>=2.4.2,<3"
+    "cython"
 ]
 build-backend = "setuptools.build_meta"
 py_modules=["ppanggolin"]
@@ -57,6 +46,11 @@ doc = [
     "myst-parser==2",
     "docutils==0.18.1",
     "sphinxcontrib.mermaid==0.9.2",
+]
+test = [
+    "pytest>=7.0.0"
+]
+python_deps = [
     "tqdm>=4.64",
     "tables>=3.7",
     "pyrodigal>=3.0.1",
@@ -69,9 +63,6 @@ doc = [
     "numpy>=1.24",
     "bokeh>=2.4.2,<3"
 ]
-test = [
-    "pytest>=7.0.0"
-]
 #
 [project.urls]
 Homepage = "https://labgem.genoscope.cns.fr/2023/04/27/ppanggolin/"

From 7bfc3b2248e77a49096d6441a542ad79d8c09748 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 10:46:44 +0100
Subject: [PATCH 16/23] clean readthedocs

---
 .readthedocs.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 92e946c5..11afb0d3 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -17,10 +17,6 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.8"
-#     python: "mambaforge-22.9"
-
-# conda:
-#   environment: ppanggolin_env.yaml
 
   
 # Build documentation in the "docs/" directory with Sphinx

From 3264b124c441523000c925b7cc9a5da0a9e3a460 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 10:55:51 +0100
Subject: [PATCH 17/23] update check doc gh action

---
 .github/workflows/check_doc.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check_doc.yml b/.github/workflows/check_doc.yml
index 165fbca9..f2613ea2 100644
--- a/.github/workflows/check_doc.yml
+++ b/.github/workflows/check_doc.yml
@@ -11,7 +11,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.8'
+    - run: pip install .[doc,python_deps]
+
     # Standard drop-in approach that should work for most people.
     - uses: ammaraskar/sphinx-action@master
       with:

From 12c79432cfb1fe192be80837f971d629adbe709d Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 11:00:15 +0100
Subject: [PATCH 18/23] update check doc gh action

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

diff --git a/.github/workflows/check_doc.yml b/.github/workflows/check_doc.yml
index f2613ea2..2b009f7f 100644
--- a/.github/workflows/check_doc.yml
+++ b/.github/workflows/check_doc.yml
@@ -4,6 +4,7 @@ on:
   push:
     paths:
       - 'docs/**'
+      - '.readthedocs.yaml'
 
 jobs:
   build:

From cc85c051e7a1166e666236d48416246f297cbd82 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 11:01:21 +0100
Subject: [PATCH 19/23] fix makefile

---
 docs/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Makefile b/docs/Makefile
index d0c3cbf1..ed880990 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+SOURCEDIR     = .
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".

From d4251c0bf42943c3122f58c1d0295184554d9947 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 11:25:07 +0100
Subject: [PATCH 20/23] update check doc action

---
 .github/workflows/check_doc.yml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/check_doc.yml b/.github/workflows/check_doc.yml
index 2b009f7f..9ca53ff5 100644
--- a/.github/workflows/check_doc.yml
+++ b/.github/workflows/check_doc.yml
@@ -5,7 +5,8 @@ on:
     paths:
       - 'docs/**'
       - '.readthedocs.yaml'
-
+      - '.github/workflows/check_doc.yml'
+      
 jobs:
   build:
 
@@ -14,15 +15,16 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
+      name: install ppanggolin with python deps and doc deps
       with:
         python-version: '3.8'
     - run: pip install .[doc,python_deps]
 
-    # Standard drop-in approach that should work for most people.
-    - uses: ammaraskar/sphinx-action@master
-      with:
-        docs-folder: "docs/"
-        build-command: "sphinx-build -b html . build/"
+    - name: Complete workflow
+      shell: bash -l {0}
+      run: |
+        cd docs/
+        sphinx-build -b html . build/
     # Great extra actions to compose with:
     # Create an artifact of the html output.
     - uses: actions/upload-artifact@v1

From 7b2e7bab27f155856a106d10635c09af38520d6a Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 11:28:04 +0100
Subject: [PATCH 21/23] fix step name in gh action

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

diff --git a/.github/workflows/check_doc.yml b/.github/workflows/check_doc.yml
index 9ca53ff5..5e8b43f0 100644
--- a/.github/workflows/check_doc.yml
+++ b/.github/workflows/check_doc.yml
@@ -6,7 +6,7 @@ on:
       - 'docs/**'
       - '.readthedocs.yaml'
       - '.github/workflows/check_doc.yml'
-      
+
 jobs:
   build:
 
@@ -15,10 +15,10 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
-      name: install ppanggolin with python deps and doc deps
       with:
         python-version: '3.8'
-    - run: pip install .[doc,python_deps]
+    - name: install ppanggolin with python deps and doc deps
+      run: pip install .[doc,python_deps]
 
     - name: Complete workflow
       shell: bash -l {0}

From 1feaacf2478348197738621601393bd8dd17d6dc Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 11:55:05 +0100
Subject: [PATCH 22/23] update api doc

---
 docs/api/modules.md            |  8 --------
 docs/api/ppanggolin.formats.md | 13 +++++++++++--
 docs/index.md                  | 12 +-----------
 3 files changed, 12 insertions(+), 21 deletions(-)
 delete mode 100644 docs/api/modules.md

diff --git a/docs/api/modules.md b/docs/api/modules.md
deleted file mode 100644
index 6e569604..00000000
--- a/docs/api/modules.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# API Reference
-
-```{toctree}
-:maxdepth: 2
-ppanggolin
-indice_and_table
-```
-
diff --git a/docs/api/ppanggolin.formats.md b/docs/api/ppanggolin.formats.md
index 5f9ec7ae..a13be3db 100644
--- a/docs/api/ppanggolin.formats.md
+++ b/docs/api/ppanggolin.formats.md
@@ -29,10 +29,19 @@
    :show-inheritance:
 ```
 
-## ppanggolin.formats.writeFlat module
+## ppanggolin.formats.writeFlatGenomes module
 
 ```{eval-rst}
-.. automodule:: ppanggolin.formats.writeFlat
+.. automodule:: ppanggolin.formats.writeFlatGenomes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
+## ppanggolin.formats.writeFlatPangenome module
+
+```{eval-rst}
+.. automodule:: ppanggolin.formats.writeFlatPangenome
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/index.md b/docs/index.md
index de7135a5..2ffd38c2 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -86,15 +86,5 @@ user/metadata
 
 dev/contribute
 dev/buildDoc
-api/modules
+api/api_ref
 ```
-
-
-# Indices and tables
-[//]: # (- {ref}`ppanggolin package`)
-
-- {ref}`genindex`
-
-- {ref}`modindex`
-
-- {ref}`search`

From d896a14bd8690ab38bbdaaed2846ebcc92bab196 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Tue, 19 Dec 2023 11:55:50 +0100
Subject: [PATCH 23/23] add entry point for the api doc

---
 docs/api/api_ref.md | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 docs/api/api_ref.md

diff --git a/docs/api/api_ref.md b/docs/api/api_ref.md
new file mode 100644
index 00000000..6e569604
--- /dev/null
+++ b/docs/api/api_ref.md
@@ -0,0 +1,8 @@
+# API Reference
+
+```{toctree}
+:maxdepth: 2
+ppanggolin
+indice_and_table
+```
+