Feature/sensitivity curve

.gitignore

@@ -101,3 +101,5 @@ ENV/
 .mypy_cache/
 *.root
 *.png
+*.pdf
+*.DS_Store

.readthedocs.yaml

@@ -0,0 +1,31 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: documentation/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: documentation/requirements.txt

Dockerfile

@@ -24,6 +24,7 @@ RUN mkdir -p $MERMITHID_BUILD_PREFIX &&\
 
 RUN source $COMMON_BUILD_PREFIX/setup.sh &&\
     pip install iminuit &&\
+    pip install numericalunits &&\
     /bin/true
 
 ########################

README.md

@@ -6,7 +6,7 @@ Mermithid is an extension of [morpho](https://github.com/morphoorg/morpho) that
 
 ## Requirements
 
-You will need to install via a package manager (such as apt-get):
+If you are not using a container with pre-installed dependencies, you will need to install via a package manager (such as apt-get):
 
 - python (3.x; 2.7.x support not guaranteed)
 - python-pip
@@ -15,10 +15,15 @@ You will need to install via a package manager (such as apt-get):
 
 ## Installation
 
+After cloning mermithid, run `git submodule update --init --recursive`.
+
 These are two possible ways of installing and working with mermithid.
 
 ### Virtual environment installation
 
+Before installing, clone subdirecories recursively: ``git submodule update --init --recursive``.
+<br>Then install mermithid in your environment:
+
 1. Cicada and Phylloxera need to be installed in a sub directory:
 
   ```bash
@@ -45,16 +50,24 @@ These are two possible ways of installing and working with mermithid.
 
 ### Docker installation
 
-Docker provides a uniform test bed for development and bug testing. Please use this environment to testing/resolving bugs.
+Create a docker image and start a mermithid container
 
 1. Install Docker (Desktop version): <https://docs.docker.com/engine/installation/>
-2. Clone and pull the latest master version of mermithid
-3. Inside the mermithid folder, execute `docker-compose run mermithid`. The container prompter should appear at the end of the installation. A directory (`mermithid_share`) should be created in your home and mounted under the `/host` folder: you can modify this by editing the docker-compose file.
-4. When reinstalling, you can remove the image using `docker rmi mermithid_mermithid`
+3. Clone and pull the latest main version of mermithid or the feature branch you want to work with
+4. Go to the cloned directory: ``cd mermithid``
+5. Pull the submodules: ``git submodule update --init --recursive``
+6. Build docker image: ``docker build --no-cache -t mermithid:<tag> .``
+7. To start the container and mount a directory for data sharing with your host into the container do: 
+<br>```docker run --rm -it -v ~/mermithid_share:/host mermithid:<tag> /bin/bash```
+
+An alternative to steps 6 and 7 is to use docker-compose by executing: ``docker-compose run mermithid``.
+
+<br>In both cases files saved in ```/host``` are shared with the host in ```~/mermithid_share```.
+
 
 ### Running mermithid
 
-In both cases, you need to set the paths right for using these software. For example in the docker container:
+For running mermithid you need to set the paths right for using these software. For example in the docker container:
 
 ```bash
 source $MERMITHID_BUILD_PREFIX/setup.sh
@@ -64,4 +77,11 @@ source $MERMITHID_BUILD_PREFIX/bin/this_phylloxera.sh
 
 ## Quick start and examples
 
-Mermithid works a-la morpho, where the operations on data are defined using processors. Each processor should be defined with a name, then should have its attributes configured using a dictionary before being run. Examples of how to use mermithid can be found in the "tests" folder.
+Mermithid works a-la morpho, where the operations on data are defined using processors. Each processor should be defined with a name, then should have its attributes configured using a dictionary before being run. Examples of how to use mermithid can be found in the "tests" and the "test_analysis" folders.
+
+
+## Easy development
+
+To develop mermithid without having to rebuild the container, share the repository on the host with the container by starting it with: ```docker run --rm -it -v ~/mermithid_share:/host -v ~/repos/mermithid:/mermithid mermithid:<tag> /bin/bash```. This assumes that mermithid was cloned to ``~/repos``.
+
+After sourcing the setup scripts, modify the PYTHONPATH: ```export PYTHONPATH=/mermithid:$PYTHONPATH```. Now changes made on the host will directly be used by the container.

docker-compose.yaml

@@ -1,9 +1,40 @@
-version: "3"
 
+#version: "3.9"
+
+# Check running containers docker ps (detached) -d
+#docker compose up -d 
+
+# Attach to container docker attach [name]
+#docker attach mermithid_sensitivity
+
+# Mermithid is a bind mount, this guarantees: live code edits on host, Python imports always resolve to your branch & no accidental use of the installed site-packages version
+#export PYTHONPATH=/mermithid/:$PYTHONPATH &&
+
+# /mermithid is on sys.path. Python should import from it but it does not, because mermithid is already imported earlier by ROOT’s import hook. Once a module is loaded, Python never re-resolves it.
+# environment: is already working. It just can’t solve this class of problem. PYTHONPATH is correct; ROOT imports mermithid first and locks it in — only an editable install can override that.
+#environment: #- PYTHONPATH=/mermithid:${PYTHONPATH}
+# Overriding sys for PYTHONPATH
 services:
   mermithid:
-    build: .
-    command: "/bin/bash"
+    image: mermithid:sensitivity_branch
+    container_name: mermithid_sensitivity
+    stdin_open: true       # Interactive search
+    tty: true              # Allocate TTY
     volumes:
-      # share a subdirectory from the host to /host in the docker (can be edited)
-      - ~/mermithid_share:/host
+      - ~/repos/mermithid:/mermithid
+      - ~/repos/mermithid_share:/host_data
+      - ~/repos/termite:/termite
+    command: >
+      bash -lic "
+        source /usr/local/p8/mermithid/v1.2.3/setup.sh &&
+        source /usr/local/p8/mermithid/v1.2.3/bin/this_phylloxera.sh &&
+        source /usr/local/p8/mermithid/v1.2.3/bin/this_cicada.sh &&
+        pip install -e /mermithid &&
+        bash
+      "
+#bash -c "
+#source /usr/local/p8/mermithid/v1.2.3/setup.sh &&
+#source /usr/local/p8/mermithid/v1.2.3/bin/this_phylloxera.sh &&
+#source /usr/local/p8/mermithid/v1.2.3/bin/this_cicada.sh &&
+#exec bash
+#"

documentation/Makefile

@@ -8,8 +8,6 @@ SPHINXPROJ    = mermithid
 SOURCEDIR     = .
 BUILDDIR      = build
 
-PY_CMD = import better_apidoc; better_apidoc.main(['better_apidoc','-t', '_templates','--force','--separate','-o','better_apidoc_out','../$(SPHINXPROJ)'])  # overwrite existing files
-APIDOC_CMD = python -c "$(PY_CMD)"
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -22,5 +20,3 @@ help:
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-betterapi:
-	@$(APIDOC_CMD)