Fix binder (#40)

* Add explicit binder dockerfile

* Add fix_gdal

* Put docker context to root

Author: danlooo

.binder/Manifest.toml

@@ -0,0 +1 @@
+.gitignore

.binder/Project.toml

@@ -0,0 +1,42 @@
+# repo2docker without this Dockerfile would throw ArgumentError: Package OpenSSL_jll is required
+# despite being part of Project.toml. This issue is specific to RQADeforestation.jl
+
+FROM debian:stable-slim AS base
+ENV JULIA_VERSION=1.11.4
+COPY env/apt.txt .
+RUN \
+    # base
+    apt-get update && \
+    apt-get install -y wget && \
+    cat apt.txt | xargs apt-get install -y && \
+    # conda
+    wget -O miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py312_25.1.1-2-Linux-x86_64.sh && \
+    mkdir -p /root/.conda && \
+    bash miniconda.sh -b -p /root/miniconda3 && \
+    rm -f miniconda.sh && \
+    /root/miniconda3/bin/conda init && \
+    # julia
+    wget -O julia.tar.gz https://julialang-s3.julialang.org/bin/linux/x64/1.11/julia-${JULIA_VERSION}-linux-x86_64.tar.gz && \
+    tar zxvf julia.tar.gz && \
+    mv julia-${JULIA_VERSION} /usr/local/lib/julia && \
+    ln -s /usr/local/lib/julia/bin/julia /usr/local/bin/
+ENV PATH="/root/miniconda3/bin:$PATH"
+
+FROM base AS python
+COPY env/environment.yml .
+RUN conda env update --file environment.yml --prune --name base
+
+FROM base AS julia
+COPY env/Project.toml /root/.julia/environments/v1.11/Project.toml
+COPY env/Manifest.toml /root/.julia/environments/v1.11/Manifest.toml
+RUN julia -e 'using Pkg; Pkg.instantiate(); Pkg.status()'
+
+FROM base AS final
+WORKDIR /work
+COPY --from=python /root/miniconda3/ /root/miniconda3/
+COPY --from=julia /usr/local/bin/julia /usr/local/bin/julia
+COPY --from=julia /usr/local/lib/julia /usr/local/lib/julia
+COPY --from=julia /root/.julia /root/.julia
+COPY env/fix_gdal.sh .
+RUN bash fix_gdal.sh
+CMD ["jupyter", "notebook", "--allow-root"]

.binder/apt.txt

@@ -0,0 +1,42 @@
+# FAIRSEND meeting 2025-05-08
+
+- bids paper submitted
+
+## Software readiness review
+
+- scheduled on 2025-06-19
+- ensure that the workflow works on our machine (eodc VM)
+- no template with formal requirements
+- Stephan needs to write as well
+
+- Date: week before lps, 18.6.25?, doodle: 16,17,18,20
+
+## Meeting with EODC
+
+- Asked poll to find a date on 28.4. at https://dud-poll.inf.tu-dresden.de/aCcu2iUisQ/
+- No one replied. Did I do sth. wrong? (holiday black hole...)
+- Invited Christian Briese, since he did not respond, lets just do another poll :)
+- Service readyness review is in Augus
+
+- neues doodle: Fransika König, [email protected]
+- nächste 2 wochen
+
+## ESA living planets poster
+
+- We have 2 posters accepted
+- send drafts to zaynab until end of may
+- BGC prints them
+- 23—27 JUNE 2025 VIENNA, AUSTRIA
+- LPS did not publish a poster template yet
+- Going: Daniel, Felix
+
+## Next steps: To Do in May
+
+- Any major tasks required for deployment?
+- Daniel: draft workflow poster
+- Felix: draft algo poster -> update existing one
+- Stephan: draft software readiness report
+
+# Stephan
+
+- stat. kompliierung zu openEO, felix schreibt an

.binder/environment.yml

@@ -13,7 +13,6 @@ This repository contains code and documentation for a FAIR workflow based on the
 | -------------------------------------------- | ------------------------------------------------------------------------------------------------ |
 | [`RQADeforestation.jl`](RQADeforestation.jl) | git submodule to the underlying Julia package                                                    |
 | [`infrastructure`](infrastructure)           | VM setup description using Terraform                                                             |
-| [`ogc-api`](ogc-api)                         | OGC API using pygeoapi                                                                           |
 | [`ogc-app-cwl`](ogc-app-cwl)                 | OGC Application Package as a CWL workflow                                                        |
 | [`website`](website)                         | [Project website](https://earthyscience.github.io/FAIRSenDD) with documentation and workflow GUI |
 

.binder/install.R

@@ -0,0 +1,7 @@
+*
+!*.toml
+!*.yml
+!apt.txt
+!*.sh
+!Dockerfile
+!.gitignore